Notice (8): Undefined variable: source_groups_information [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ), 'data_type' => 'gene_family', 'gf_id' => 'ORTHO05D005089', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ) $data_type = 'gene_family' $gf_id = 'ORTHO05D005089' $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'ORTHO05D005089' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 151
<label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
<label>Source(s)</label>
<select class='form form-select' name='ontology_source_group' id='ontology_source_group'>
<?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ), 'data_type' => 'gene_family', 'gf_id' => 'ORTHO05D005089', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ) $data_type = 'gene_family' $gf_id = 'ORTHO05D005089' $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'ORTHO05D005089' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' )
include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 151
Notice (8): Trying to access array offset on value of type null [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ), 'data_type' => 'gene_family', 'gf_id' => 'ORTHO05D005089', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ) $data_type = 'gene_family' $gf_id = 'ORTHO05D005089' $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'ORTHO05D005089' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 151
Warning (2): Invalid argument supplied for foreach() [APP/View/Tools/similarity_heatmap.ctp, line 77]Code Context <label>Source(s)</label> <select class='form form-select' name='ontology_source_group' id='ontology_source_group'> <?php foreach ($source_groups_information['available'] as $source_group_id) : ?> $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Tools/similarity_heatmap.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'gene_selection' => array( 'parameters' => array( (int) 0 => array( [maximum depth reached] ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ), 'data_type' => 'gene_family', 'gf_id' => 'ORTHO05D005089', 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'subfamily_family_types' => array( (int) 0 => 'ORTHOFAM' ), 'parental_family_types' => array( (int) 0 => 'HOMFAM' ), 'gene_family_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'allowed_data_types' => array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) ) $sidebar_info = array( 'gf_id' => 'ORTHO05D005089', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '164', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $gene_selection = array( 'parameters' => array( (int) 0 => array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' ) ), 'genes' => array( 'A09p35900' => 'bna', 'Aa31LG10G6590' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2193' => 'aag', 'Actinidia01578' => 'ach', 'Actinidia12522' => 'ach', 'Actinidia33709' => 'ach', 'Ah.03g146620' => 'amhyb', 'Ah.09g232250' => 'amhyb', 'AL1G44580' => 'aly', 'Aqoxy1G01576' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8V1VF7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQL6P1' => 'arhy', 'AT1G30540' => 'ath', 'ATR0165G021' => 'atr', 'Atru.chr10.841' => 'acertr', 'Atru.chr6.2011' => 'acertr', 'Atru.chr6.2012' => 'acertr', 'BcaB07g32666' => 'bca', 'BcaB07g32690' => 'bca', 'BcaB07g32692' => 'bca', 'BcaC05g27075' => 'bca', 'BolC5t31687H' => 'bol', 'BraA09t39115Z' => 'bra', 'C05p29560' => 'bna', 'CAN.G1316.2' => 'can', 'CAN.G304.4' => 'can', 'CANSAT35G0713' => 'cansat', 'CANSAT64G0449' => 'cansat', 'CARHR029950' => 'chi', 'Carub.0001s2880' => 'cru', 'CBR_g20100' => 'cbr', 'Cc05_g00540' => 'ccan', 'Cc09_g07890' => 'ccan', 'CDE04G1567' => 'cde', 'Cfa000809' => 'cfa', 'Cfa023541' => 'cfa', 'Cfa023542' => 'cfa', 'Ciclev10031991m.g' => 'ccl', 'CiPaw.03G190700' => 'cil', 'CiPaw.10G109400' => 'cil', 'ClCG07G010830' => 'cla', 'ClCG11G016660' => 'cla', 'COL.COLO4_29897' => 'col', 'Cpa.g.sc1123.2' => 'cpa', 'Cre17.g720528' => 'cre', 'CsaV3_4G007480' => 'csa', 'CsaV3_4G032170' => 'csa', 'CSS0023242' => 'camsi', 'CSS0039894' => 'camsi', 'DCAR_007839' => 'dca', 'DCAR_013332' => 'dca', 'Dinv05044' => 'din', 'Dinv10789' => 'din', 'Duzib147G0966' => 'dzi', 'Duzib264G0097' => 'dzi', 'ECA248G0068' => 'eca', 'Eucgr.A00888' => 'egr', 'FAN05G3231' => 'fan', 'FAN14G1093' => 'fan', 'FvH4_6g39150' => 'fve', 'Glyma.02G281300' => 'gma', 'Glyma.14G033300' => 'gma', 'Gohir.A05G380500' => 'ghi', 'Gohir.D04G035100' => 'ghi', 'Gorai.012G039600' => 'gra', 'GSVIVG01020802001' => 'vvi', 'GSVIVG01021661001' => 'vvi', 'HanXRQChr01g0023901' => 'han', 'HanXRQChr04g0115031' => 'han', 'HanXRQChr14g0432981' => 'han', 'Haze_05859' => 'cav', 'Haze_05864' => 'cav', 'Haze_13622' => 'cav', 'Hma1.2p1_0067F.1_g036930' => 'hma', 'Hma1.2p1_0067F.1_g036960' => 'hma', 'Hma1.2p1_0583F.1_g183050' => 'hma', 'HPP92_005880' => 'vpl', 'Hund21563' => 'sun', 'Hund21564' => 'sun', 'Lalb_Chr10g0106401' => 'lal', 'Lj1A584G30' => 'lonja', 'Lj2A329G54' => 'lonja', 'LjContig00049g0028236' => 'lja', 'Lsat_1_v5_gn_1_77721' => 'lsa', 'Lsat_1_v5_gn_1_91760' => 'lsa', 'Lsat_1_v5_gn_2_30700' => 'lsa', 'Manes.01G131701' => 'mes', 'Manes.01G131702' => 'mes', 'Manes.02G090600' => 'mes', 'Manes.14G123700' => 'mes', 'Mapoly0122s0046' => 'mpo', 'MBI02_g32064_MAGBIO' => 'mbi', 'MBI18_g11296_MAGBIO' => 'mbi', 'MCO07G054' => 'mco', 'MD09G1144800' => 'mdo', 'MD17G1131300' => 'mdo', 'Medtr5g090130' => 'mtr', 'MELO3C016194.2' => 'cme', 'MELO3C026388.2' => 'cme', 'Migut.H01268' => 'egut', 'Migut.M01899' => 'egut', 'MSTRG.16294' => 'ama', 'Nitab4.5_0000076g0250' => 'nta', 'Nitab4.5_0001843g0170' => 'nta', 'Nitab4.5_0006724g0010' => 'nta', 'Nitab4.5_0011274g0010' => 'nta', 'Nn3g20219' => 'nnu', 'Oeu015176.1' => 'oeu', 'Oeu041105.1' => 'oeu', 'Oeu044867.2' => 'oeu', 'Os07g0147700' => 'osa', 'Os09g0133700' => 'osa', 'Peaxi162Scf00351g00818' => 'pax', 'Peaxi162Scf00395g00318' => 'pax', 'PGR031G0720' => 'pgr', 'PGSC0003DMG400021156' => 'stu', 'PGSC0003DMG401028079' => 'stu', 'Phvul.008G199600' => 'pvu', 'Potri.001G466900' => 'ptr', 'Potri.011G164500' => 'ptr', 'Potri.014G143500' => 'ptr', 'Pp3c17_6390' => 'ppa', 'PRCOL_00003495' => 'pco', 'Prupe.3G183100' => 'ppe', 'Psat2g018080' => 'psa', 'PSO541G6471' => 'pso', 'PSO675G7088' => 'pso', 'QL04p059944' => 'qlo', 'QL05p061983' => 'qlo', 'QL05p062039' => 'qlo', 'RcHm_v2.0_Chr2g0152961' => 'rch', 'Rhsim13G0121900' => 'rsi', 'Sabra11G0140700' => 'sbr', 'Sabra14G0108500' => 'sbr', 'Sabra16G0316700' => 'sbr', 'SalBow8G0183' => 'sbo', 'Sc10g0005420' => 'sci', 'Sed0001791' => 'sed', 'Sed0020733' => 'sed', 'SEGI_10868' => 'sgi', 'SEGI_21833' => 'sgi', 'SEGI_40766' => 'sgi', 'SGA_v2.0_scaffold223G42867' => 'sas', 'SHI10516' => 'shi', 'SMO334G0132' => 'smo', 'Solyc02g023980.3' => 'sly', 'Solyc07g044750.3' => 'sly', 'Sopen02g006690' => 'spe', 'Sopen07g023340' => 'spe', 'Sp1g26410' => 'spa', 'TAR624G0620' => 'tar', 'TAR629G1010' => 'tar', 'THA.LOC104798598' => 'tha', 'Thecc.01G165100' => 'tca', 'Thhalv10008046m.g' => 'esa', 'TPR.G24734' => 'tpr', 'TWI14G0586' => 'twi', 'TWI59G1372' => 'twi', 'unitig_37.g12072' => 'ugi', 'vmacro03380' => 'vma', 'VMungo0647G0619' => 'vmu', 'Zm00001eb058170' => 'zma', 'Zm00001eb261810' => 'zma', 'Zm00001eb299940' => 'zma' ) ) $data_type = 'gene_family' $gf_id = 'ORTHO05D005089' $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D005089' ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $subfamily_family_types = array( (int) 0 => 'ORTHOFAM' ) $parental_family_types = array( (int) 0 => 'HOMFAM' ) $gene_family_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $allowed_data_types = array( 'GO' => 'Gene Ontology', 'INTERPRO' => 'InterPro', 'GENE_FAMILY' => 'Gene Family' ) $data_identifier_value = 'ORTHO05D005089' $data_identifier_description = '' $adt_title = 'Gene Family' $adt = 'GENE_FAMILY' $is_selected = 'selected='selected'' $parameter = array( 'data_type' => 'GENE_FAMILY', 'data_value' => 'ORTHO05D005089' )include - APP/View/Tools/similarity_heatmap.ctp, line 77 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200 Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167 [main] - APP/webroot/index.php, line 151