If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 44 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ), 'gf_id' => 'HOM05D001828', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001828' ), 'data_identifier' => 'HOM05D001828', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001828', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '359', 'num_species' => '26' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'arahy.Tifrunner.gnm1.ann1.B2M0SA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CYZ3KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA5ZC6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NN1I39' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V6U7IH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X9YRJ7' => 'arhy', 'Atru.chr10.37' => 'acertr', 'Atru.chr10.43' => 'acertr', 'Atru.chr9.1' => 'acertr', 'Atru.chr9.218' => 'acertr', 'Atru.ctg1432.20' => 'acertr', 'Atru.ctg1432.35' => 'acertr', 'BcaC06g35653' => 'bca', 'BcaC06g36786' => 'bca', 'BcaNung06430' => 'bca', 'C07p12580' => 'bna', 'CAN.G3389.1' => 'can', 'CDE02G0001' => 'cde', 'CDE02G2883' => 'cde', 'CDE02G3303' => 'cde', 'Cpa.g.sc978.2' => 'cpa', 'CsaV3_2G020820' => 'csa', 'CsaV3_2G020830' => 'csa', 'CSS0027849' => 'camsi', 'CSS0030230' => 'camsi', 'CSS0047100' => 'camsi', 'CSS0047713' => 'camsi', 'CSS0048211' => 'camsi', 'Duzib093G0517' => 'dzi', 'Duzib093G2160' => 'dzi', 'Duzib151G0577' => 'dzi', 'Duzib217G0002' => 'dzi', 'Duzib250G0005' => 'dzi', 'EL10Ac2g03013' => 'bvu', 'EL10As7g23711' => 'bvu', 'FAN08G2289' => 'fan', 'FAN08G2444' => 'fan', 'LjContig00092g0015566' => 'lja', 'LjContig00371g0019658' => 'lja', 'LjContig00372g0002420' => 'lja', 'Medtr0052s0110' => 'mtr', 'Medtr0055s0130' => 'mtr', 'Medtr5g031940' => 'mtr', 'Nn038s41647' => 'nnu', 'Nn038s41669' => 'nnu', 'Nn038s41692' => 'nnu', 'Nn040s41717' => 'nnu', 'Nn040s41739' => 'nnu', 'Nn040s41762' => 'nnu', 'Nn040s41785' => 'nnu', 'Nn046s41837' => 'nnu', 'Nn046s41860' => 'nnu', 'Nn046s41883' => 'nnu', 'Nn046s41906' => 'nnu', 'Nn058s41946' => 'nnu', 'Nn058s41969' => 'nnu', 'Nn058s41991' => 'nnu', 'Nn059s42010' => 'nnu', 'Nn059s42033' => 'nnu', 'Nn059s42056' => 'nnu', 'Nn061s42086' => 'nnu', 'Nn061s42109' => 'nnu', 'Nn061s42132' => 'nnu', 'Nn062s42142' => 'nnu', 'Nn062s42165' => 'nnu', 'Nn062s42187' => 'nnu', 'Nn067s42246' => 'nnu', 'Nn067s42268' => 'nnu', 'Nn067s42291' => 'nnu', 'Nn069s42302' => 'nnu', 'Nn069s42327' => 'nnu', 'Nn069s42350' => 'nnu', 'Nn072s42415' => 'nnu', 'Nn072s42437' => 'nnu', 'Nn072s42459' => 'nnu', 'Nn076s42486' => 'nnu', 'Nn076s42509' => 'nnu', 'Nn077s42544' => 'nnu', 'Nn077s42568' => 'nnu', 'Nn077s42591' => 'nnu', 'Nn078s42622' => 'nnu', 'Nn078s42644' => 'nnu', 'Nn078s42667' => 'nnu', 'Nn085s42694' => 'nnu', 'Nn085s42718' => 'nnu', 'Nn085s42719' => 'nnu', 'Nn085s42741' => 'nnu', 'Nn087s42763' => 'nnu', 'Nn087s42786' => 'nnu', 'Nn087s42807' => 'nnu', 'Nn090s42826' => 'nnu', 'Nn090s42849' => 'nnu', 'Nn090s42870' => 'nnu', 'Nn094s42908' => 'nnu', 'Nn094s42931' => 'nnu', 'Nn095s42963' => 'nnu', 'Nn095s42985' => 'nnu', 'Nn095s43007' => 'nnu', 'Nn097s43017' => 'nnu', 'Nn097s43042' => 'nnu', 'Nn097s43064' => 'nnu', 'Nn098s43074' => 'nnu', 'Nn098s43097' => 'nnu', 'Nn098s43120' => 'nnu', 'Nn104s43138' => 'nnu', 'Nn104s43164' => 'nnu', 'Nn105s43201' => 'nnu', 'Nn105s43223' => 'nnu', 'Nn108s43268' => 'nnu', 'Nn108s43290' => 'nnu', 'Nn110s43328' => 'nnu', 'Nn110s43351' => 'nnu', 'Nn115s43377' => 'nnu', 'Nn116s43387' => 'nnu', 'Nn119s43432' => 'nnu', 'Nn119s43455' => 'nnu', 'Nn122s43476' => 'nnu', 'Nn122s43500' => 'nnu', 'Nn122s43522' => 'nnu', 'Nn124s43529' => 'nnu', 'Nn124s43553' => 'nnu', 'Nn124s43575' => 'nnu', 'Nn125s43584' => 'nnu', 'Nn125s43608' => 'nnu', 'Nn125s43630' => 'nnu', 'Nn126s43639' => 'nnu', 'Nn126s43662' => 'nnu', 'Nn127s43699' => 'nnu', 'Nn129s43707' => 'nnu', 'Nn129s43731' => 'nnu', 'Nn130s43763' => 'nnu', 'Nn130s43785' => 'nnu', 'Nn136s43811' => 'nnu', 'Nn136s43835' => 'nnu', 'Nn137s43870' => 'nnu', 'Nn137s43893' => 'nnu', 'Nn139s43921' => 'nnu', 'Nn139s43943' => 'nnu', 'Nn141s43969' => 'nnu', 'Nn141s43991' => 'nnu', 'Nn142s44012' => 'nnu', 'Nn142s44034' => 'nnu', 'Nn143s44041' => 'nnu', 'Nn143s44065' => 'nnu', 'Nn148s44096' => 'nnu', 'Nn148s44120' => 'nnu', 'Nn151s44160' => 'nnu', 'Nn151s44182' => 'nnu', 'Nn152s44206' => 'nnu', 'Nn152s44228' => 'nnu', 'Nn153s44254' => 'nnu', 'Nn154s44279' => 'nnu', 'Nn157s44317' => 'nnu', 'Nn157s44339' => 'nnu', 'Nn159s44363' => 'nnu', 'Nn159s44386' => 'nnu', 'Nn165s44403' => 'nnu', 'Nn165s44426' => 'nnu', 'Nn167s44460' => 'nnu', 'Nn167s44482' => 'nnu', 'Nn175s44516' => 'nnu', 'Nn175s44530' => 'nnu', 'Nn177s44539' => 'nnu', 'Nn177s44563' => 'nnu', 'Nn178s44585' => 'nnu', 'Nn178s44609' => 'nnu', 'Nn185s44627' => 'nnu', 'Nn185s44651' => 'nnu', 'Nn188s44681' => 'nnu', 'Nn188s44703' => 'nnu', 'Nn189s44710' => 'nnu', 'Nn189s44734' => 'nnu', 'Nn190s44771' => 'nnu', 'Nn194s44795' => 'nnu', 'Nn194s44819' => 'nnu', 'Nn195s44831' => 'nnu', 'Nn196s44854' => 'nnu', 'Nn196s44876' => 'nnu', 'Nn1g00034' => 'nnu', 'Nn1g07901' => 'nnu', 'Nn200s44901' => 'nnu', 'Nn201s44925' => 'nnu', 'Nn201s44949' => 'nnu', 'Nn202s44973' => 'nnu', 'Nn203s44999' => 'nnu', 'Nn203s45023' => 'nnu', 'Nn204s45049' => 'nnu', 'Nn207s45077' => 'nnu', 'Nn207s45099' => 'nnu', 'Nn208s45106' => 'nnu', 'Nn208s45130' => 'nnu', 'Nn209s45135' => 'nnu', 'Nn209s45158' => 'nnu', 'Nn210s45173' => 'nnu', 'Nn213s45227' => 'nnu', 'Nn217s45250' => 'nnu', 'Nn217s45275' => 'nnu', 'Nn220s45307' => 'nnu', 'Nn221s45328' => 'nnu', 'Nn222s45373' => 'nnu', 'Nn223s45387' => 'nnu', 'Nn223s45409' => 'nnu', 'Nn224s45431' => 'nnu', 'Nn227s45468' => 'nnu', 'Nn229s45498' => 'nnu', 'Nn230s45536' => 'nnu', 'Nn236s45575' => 'nnu', 'Nn237s45612' => 'nnu', 'Nn238s45637' => 'nnu', 'Nn240s45673' => 'nnu', 'Nn242s45694' => 'nnu', 'Nn244s45742' => 'nnu', 'Nn245s45756' => 'nnu', 'Nn246s45796' => 'nnu', 'Nn247s45805' => 'nnu', 'Nn247s45829' => 'nnu', 'Nn250s45851' => 'nnu', 'Nn251s45857' => 'nnu', 'Nn252s45898' => 'nnu', 'Nn260s45932' => 'nnu', 'Nn267s45976' => 'nnu', 'Nn268s46000' => 'nnu', 'Nn272s46032' => 'nnu', 'Nn273s46037' => 'nnu', 'Nn275s46077' => 'nnu', 'Nn282s46086' => 'nnu', 'Nn284s46108' => 'nnu', 'Nn288s46162' => 'nnu', 'Nn299s46217' => 'nnu', 'Nn2g16038' => 'nnu', 'Nn306s46254' => 'nnu', 'Nn307s46259' => 'nnu', 'Nn310s46291' => 'nnu', 'Nn315s46308' => 'nnu', 'Nn318s46321' => 'nnu', 'Nn322s46326' => 'nnu', 'Nn327s46362' => 'nnu', 'Nn329s46373' => 'nnu', 'Nn338s46403' => 'nnu', 'Nn341s46420' => 'nnu', 'Nn343s46441' => 'nnu', 'Nn344s46448' => 'nnu', 'Nn347s46469' => 'nnu', 'Nn352s46483' => 'nnu', 'Nn356s46499' => 'nnu', 'Nn365s46511' => 'nnu', 'Nn398s46559' => 'nnu', 'Nn3g16073' => 'nnu', 'Nn3g16107' => 'nnu', 'Nn3g20496' => 'nnu', 'Nn3g20520' => 'nnu', 'Nn3g20542' => 'nnu', 'Nn3g20555' => 'nnu', 'Nn3g20577' => 'nnu', 'Nn3g20614' => 'nnu', 'Nn3g20838' => 'nnu', 'Nn402s46566' => 'nnu', 'Nn408s46573' => 'nnu', 'Nn422s46607' => 'nnu', 'Nn430s46637' => 'nnu', 'Nn437s46670' => 'nnu', 'Nn443s46692' => 'nnu', 'Nn4g25902' => 'nnu', 'Nn5g27012' => 'nnu', 'Nn5g27034' => 'nnu', 'Nn5g27315' => 'nnu', 'Nn5g31169' => 'nnu', 'Nn5g31191' => 'nnu', 'Nn5g31213' => 'nnu', 'Nn5g31248' => 'nnu', 'Nn5g31272' => 'nnu', 'Nn5g31283' => 'nnu', 'Nn5g31302' => 'nnu', 'Nn5g31321' => 'nnu', 'Nn5g31354' => 'nnu', 'Nn5g31383' => 'nnu', 'Nn5g31405' => 'nnu', 'Nn5g31425' => 'nnu', 'Nn5g31454' => 'nnu', 'Nn5g31481' => 'nnu', 'Nn6g32489' => 'nnu', 'Nn6g32505' => 'nnu', 'Nn6g32526' => 'nnu', 'Nn6g32548' => 'nnu', 'Nn6g32570' => 'nnu', 'Nn6g32591' => 'nnu', 'Nn6g32627' => 'nnu', 'Nn6g32654' => 'nnu', 'Nn6g32675' => 'nnu', 'Nn6g32699' => 'nnu', 'Nn6g32723' => 'nnu', 'Nn6g32733' => 'nnu', 'Nn6g32757' => 'nnu', 'Nn6g32767' => 'nnu', 'Nn6g32776' => 'nnu', 'Nn6g32810' => 'nnu', 'Nn6g32851' => 'nnu', 'Nn6g32858' => 'nnu', 'Nn6g32880' => 'nnu', 'Nn6g32913' => 'nnu', 'Nn6g32936' => 'nnu', 'Nn6g32953' => 'nnu', 'Nn6g32972' => 'nnu', 'Nn6g32990' => 'nnu', 'Nn6g33014' => 'nnu', 'Nn6g33034' => 'nnu', 'Nn6g33056' => 'nnu', 'Nn6g33084' => 'nnu', 'Nn6g33106' => 'nnu', 'Nn6g33125' => 'nnu', 'Nn6g33148' => 'nnu', 'Nn6g33167' => 'nnu', 'Nn6g33193' => 'nnu', 'Nn6g33213' => 'nnu', 'Nn6g33227' => 'nnu', 'Nn8g40314' => 'nnu', 'Nn8g40338' => 'nnu', 'Nn8g41310' => 'nnu', 'Nn8g41334' => 'nnu', 'Oeu006837.1' => 'oeu', 'Oeu020980.1' => 'oeu', 'PGSC0003DMG400027799' => 'stu', 'PGSC0003DMG400034813' => 'stu', 'PGSC0003DMG400035737' => 'stu', 'PGSC0003DMG400039639' => 'stu', 'PGSC0003DMG400041108' => 'stu', 'PGSC0003DMG400043850' => 'stu', 'PGSC0003DMG400044150' => 'stu', 'PGSC0003DMG400044154' => 'stu', 'PGSC0003DMG400044276' => 'stu', 'Psat0s1917g0080' => 'psa', 'Psat0s4411g0120' => 'psa', 'Psat3g188720' => 'psa', 'Psat3g189960' => 'psa', 'Psat5g302400' => 'psa', 'Psat6g146000' => 'psa', 'Psat7g211960' => 'psa', 'QL02p004526' => 'qlo', 'QL02p029498' => 'qlo', 'QL02p029509' => 'qlo', 'QL04p056327' => 'qlo', 'QL93p0428_0015' => 'qlo', 'RhsimUnG0208500' => 'rsi', 'Sc06g0003800' => 'sci', 'Sc14g0003600' => 'sci', 'Sed0007196' => 'sed', 'Sopen00g004060' => 'spe', 'Sopen11g013190' => 'spe', 'TAR629G3296' => 'tar', 'Thhalv10028070m.g' => 'esa', 'Thhalv10028168m.g' => 'esa', 'Thhalv10028188m.g' => 'esa', 'Thhalv10028279m.g' => 'esa', 'Thhalv10028304m.g' => 'esa', 'unitig_139.g29613' => 'ugi', 'unitig_174.g29146' => 'ugi', 'unitig_654.g34701' => 'ugi', 'unitig_826.g34297' => 'ugi', 'unitig_99.g29808' => 'ugi' ) $gf_id = 'HOM05D001828' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001828' ) $data_identifier = 'HOM05D001828' $data_type = 'gf_id' $species_gene_counts = array( 'arhy' => (int) 6, 'acertr' => (int) 6, 'bca' => (int) 3, 'bna' => (int) 1, 'can' => (int) 1, 'cde' => (int) 3, 'cpa' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dzi' => (int) 5, 'bvu' => (int) 2, 'fan' => (int) 2, 'lja' => (int) 3, 'mtr' => (int) 3, 'nnu' => (int) 276, 'oeu' => (int) 2, 'stu' => (int) 9, 'psa' => (int) 7, 'qlo' => (int) 5, 'rsi' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 1, 'spe' => (int) 2, 'tar' => (int) 1, 'esa' => (int) 5, 'ugi' => (int) 5 ) $gf_gene_species = 'ugi' $gf_gene_id = 'unitig_99.g29808' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1