If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_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' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 0
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ), 'gf_id' => 'HOM05D001738', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001738' ), 'data_identifier' => 'HOM05D001738', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001738', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '373', 'num_species' => '13' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12930' => 'bna', 'A01p36040' => 'bna', 'A01p36190' => 'bna', 'A01p36210' => 'bna', 'A02p31760' => 'bna', 'A02p32990' => 'bna', 'A02p33620' => 'bna', 'A02p33710' => 'bna', 'A04p27510' => 'bna', 'A04p28700' => 'bna', 'A04p28750' => 'bna', 'A05p31290' => 'bna', 'A06p00200' => 'bna', 'A06p37470' => 'bna', 'A06p37480' => 'bna', 'A07p23760' => 'bna', 'A08p05820' => 'bna', 'A08p08620' => 'bna', 'A08p15080' => 'bna', 'A08p18810' => 'bna', 'A08p31980' => 'bna', 'A08p32410' => 'bna', 'A09p23790' => 'bna', 'A09p40630' => 'bna', 'A09p40640' => 'bna', 'A09p63210' => 'bna', 'A09p63560' => 'bna', 'A09p64530' => 'bna', 'A09p64540' => 'bna', 'A09p64740' => 'bna', 'A09p64880' => 'bna', 'A09p64890' => 'bna', 'A10p19450' => 'bna', 'A10p21580' => 'bna', 'Aa31LG3G7570' => 'aar', 'Aa31LG4G12350' => 'aar', 'Aa31LG4G13090' => 'aar', 'Aa31LG5G19260' => 'aar', 'Aa31LG8G10860' => 'aar', 'Aa31LG8G10900' => 'aar', 'Aa31LG8G10910' => 'aar', 'Aa31LG8G11800' => 'aar', 'Aa31LG8G6310' => 'aar', 'Aa31LG8G6340' => 'aar', 'Aa31LG8G6350' => 'aar', 'Aa31LG8G6360' => 'aar', 'Aa31LG8G6370' => 'aar', 'Aa31LG8G6400' => 'aar', 'Aa31sc18G20' => 'aar', 'AL1G20200' => 'aly', 'AL1G22170' => 'aly', 'AL1G22300' => 'aly', 'AL1G22320' => 'aly', 'AL1G22350' => 'aly', 'AL1G23150' => 'aly', 'AL1G24890' => 'aly', 'AL1G25230' => 'aly', 'AL1G25470' => 'aly', 'AL1G26760' => 'aly', 'AL1G27080' => 'aly', 'AL1G37130' => 'aly', 'AL1G43860' => 'aly', 'AL1G47910' => 'aly', 'AL1G58940' => 'aly', 'AL4G18870' => 'aly', 'AL4G30220' => 'aly', 'AL5G11230' => 'aly', 'AL5G11320' => 'aly', 'AL5G11330' => 'aly', 'AL5G11340' => 'aly', 'AL5G14020' => 'aly', 'AL5G16800' => 'aly', 'AL5G22230' => 'aly', 'AL5G25310' => 'aly', 'AL5G38780' => 'aly', 'AL5G38790' => 'aly', 'AL5G45090' => 'aly', 'AL6G20830' => 'aly', 'AL6G27180' => 'aly', 'AL7G18540' => 'aly', 'AL7G18620' => 'aly', 'AL8G23030' => 'aly', 'AT1G09650' => 'ath', 'AT1G11270' => 'ath', 'AT1G12490' => 'ath', 'AT1G12855' => 'ath', 'AT1G12870' => 'ath', 'AT1G13200' => 'ath', 'AT1G14315' => 'ath', 'AT1G15015' => 'ath', 'AT1G33530' => 'ath', 'AT2G02030' => 'ath', 'AT2G05600' => 'ath', 'AT2G34280' => 'ath', 'AT3G25550' => 'ath', 'AT4G01640' => 'ath', 'AT5G10340' => 'ath', 'AT5G16285' => 'ath', 'BcaB03g11687' => 'bca', 'BcaB03g13098' => 'bca', 'BcaB03g13154' => 'bca', 'BcaB03g13155' => 'bca', 'BcaB04g18150' => 'bca', 'BcaB04g18151' => 'bca', 'BcaB04g18152' => 'bca', 'BcaB05g24330' => 'bca', 'BcaB06g28896' => 'bca', 'BcaB07g30292' => 'bca', 'BcaB07g30414' => 'bca', 'BcaB07g30416' => 'bca', 'BcaB07g30419' => 'bca', 'BcaB07g30712' => 'bca', 'BcaB07g32397' => 'bca', 'BcaB07g33225' => 'bca', 'BcaB08g34244' => 'bca', 'BcaB08g34245' => 'bca', 'BcaB08g34246' => 'bca', 'BcaB08g36508' => 'bca', 'BcaB08g36707' => 'bca', 'BcaB08g37391' => 'bca', 'BcaC01g00689' => 'bca', 'BcaC01g01546' => 'bca', 'BcaC02g07509' => 'bca', 'BcaC02g11659' => 'bca', 'BcaC03g13251' => 'bca', 'BcaC03g17149' => 'bca', 'BcaC03g17152' => 'bca', 'BcaC03g17250' => 'bca', 'BcaC04g18725' => 'bca', 'BcaC04g18744' => 'bca', 'BcaC04g19443' => 'bca', 'BcaC04g20153' => 'bca', 'BcaC04g21532' => 'bca', 'BcaC04g21963' => 'bca', 'BcaC05g25187' => 'bca', 'BcaC05g26332' => 'bca', 'BcaC05g26333' => 'bca', 'BcaC05g26334' => 'bca', 'BcaC05g28622' => 'bca', 'BcaC05g28625' => 'bca', 'BcaC05g28626' => 'bca', 'BcaC05g28635' => 'bca', 'BcaC05g28636' => 'bca', 'BcaC05g28637' => 'bca', 'BcaC05g28686' => 'bca', 'BcaC06g36748' => 'bca', 'BcaC07g37082' => 'bca', 'BcaC07g37559' => 'bca', 'BcaC07g38736' => 'bca', 'BcaC07g40150' => 'bca', 'BcaC07g40351' => 'bca', 'BcaC07g41659' => 'bca', 'BcaC07g41674' => 'bca', 'BcaC07g41803' => 'bca', 'BcaC08g43623' => 'bca', 'BcaC09g48787' => 'bca', 'BcaNung02452' => 'bca', 'BcaNung02572' => 'bca', 'BcaNung02577' => 'bca', 'BcaNung02775' => 'bca', 'BcaNung02915' => 'bca', 'BcaNung06201' => 'bca', 'BolC1t01509H' => 'bol', 'BolC1t04554H' => 'bol', 'BolC2t06345H' => 'bol', 'BolC2t11152H' => 'bol', 'BolC2t11157H' => 'bol', 'BolC2t11259H' => 'bol', 'BolC2t11273H' => 'bol', 'BolC3t20600H' => 'bol', 'BolC3t21603H' => 'bol', 'BolC4t22913H' => 'bol', 'BolC4t28107H' => 'bol', 'BolC5t31051H' => 'bol', 'BolC5t31052H' => 'bol', 'BolC5t31053H' => 'bol', 'BolC5t31054H' => 'bol', 'BolC5t33454H' => 'bol', 'BolC5t33458H' => 'bol', 'BolC5t33463H' => 'bol', 'BolC5t33468H' => 'bol', 'BolC5t33470H' => 'bol', 'BolC5t33533H' => 'bol', 'BolC5t33542H' => 'bol', 'BolC6t36114H' => 'bol', 'BolC7t40491H' => 'bol', 'BolC7t44617H' => 'bol', 'BolC8t47248H' => 'bol', 'BolC8t47900H' => 'bol', 'BolC8t49219H' => 'bol', 'BolC8t49224H' => 'bol', 'BolC8t49291H' => 'bol', 'BolC8t52209H' => 'bol', 'BolC8t52246H' => 'bol', 'BolC8t52365H' => 'bol', 'BolC8t52384H' => 'bol', 'BolC9t55442H' => 'bol', 'BolC9t55443H' => 'bol', 'BolC9t55928H' => 'bol', 'BolC9t57577H' => 'bol', 'BolC9t58433H' => 'bol', 'BolC9t58733H' => 'bol', 'BolC9t58757H' => 'bol', 'BraA01t01237Z' => 'bra', 'BraA01t03683Z' => 'bra', 'BraA01t03696Z' => 'bra', 'BraA02t08184Z' => 'bra', 'BraA02t08324Z' => 'bra', 'BraA02t08351Z' => 'bra', 'BraA02t08389Z' => 'bra', 'BraA04t18245Z' => 'bra', 'BraA04t18347Z' => 'bra', 'BraA04t18351Z' => 'bra', 'BraA05t21312Z' => 'bra', 'BraA05t21436Z' => 'bra', 'BraA05t21965Z' => 'bra', 'BraA06t23236Z' => 'bra', 'BraA06t26672Z' => 'bra', 'BraA07t30029Z' => 'bra', 'BraA08t32583Z' => 'bra', 'BraA08t32875Z' => 'bra', 'BraA08t32876Z' => 'bra', 'BraA08t33488Z' => 'bra', 'BraA08t33842Z' => 'bra', 'BraA08t35119Z' => 'bra', 'BraA08t35164Z' => 'bra', 'BraA09t37981Z' => 'bra', 'BraA09t39559Z' => 'bra', 'BraA09t41673Z' => 'bra', 'BraA09t41707Z' => 'bra', 'BraA09t41802Z' => 'bra', 'BraA09t41803Z' => 'bra', 'BraA09t41808Z' => 'bra', 'BraA10t44022Z' => 'bra', 'BraA10t44220Z' => 'bra', 'C01p15570' => 'bna', 'C01p45920' => 'bna', 'C01p46040' => 'bna', 'C02p03830' => 'bna', 'C02p50730' => 'bna', 'C02p51160' => 'bna', 'C02p51740' => 'bna', 'C02p51750' => 'bna', 'C02p51840' => 'bna', 'C03p83170' => 'bna', 'C03p92980' => 'bna', 'C03p92990' => 'bna', 'C04p12640' => 'bna', 'C04p66030' => 'bna', 'C05p23420' => 'bna', 'C05p23430' => 'bna', 'C05p47290' => 'bna', 'C05p47360' => 'bna', 'C05p47410' => 'bna', 'C05p47430' => 'bna', 'C05p47550' => 'bna', 'C05p47570' => 'bna', 'C06p10380' => 'bna', 'C06p26140' => 'bna', 'C07p00460' => 'bna', 'C07p40890' => 'bna', 'C07p59910' => 'bna', 'C08p15960' => 'bna', 'C08p16010' => 'bna', 'C08p16640' => 'bna', 'C08p46670' => 'bna', 'C08p46700' => 'bna', 'C08p47060' => 'bna', 'C08p47070' => 'bna', 'C08p48460' => 'bna', 'C09p25430' => 'bna', 'C09p30650' => 'bna', 'C09p47220' => 'bna', 'C09p55670' => 'bna', 'C09p59130' => 'bna', 'CARHR008650' => 'chi', 'CARHR008660' => 'chi', 'CARHR010320' => 'chi', 'CARHR010330' => 'chi', 'CARHR011460' => 'chi', 'CARHR013200' => 'chi', 'CARHR013580' => 'chi', 'CARHR014740' => 'chi', 'CARHR014880' => 'chi', 'CARHR015520' => 'chi', 'CARHR024930' => 'chi', 'CARHR032950' => 'chi', 'CARHR035940' => 'chi', 'CARHR062410' => 'chi', 'CARHR099040' => 'chi', 'CARHR100360' => 'chi', 'CARHR102530' => 'chi', 'CARHR119930' => 'chi', 'CARHR124000' => 'chi', 'CARHR125660' => 'chi', 'CARHR125670' => 'chi', 'CARHR144650' => 'chi', 'CARHR146470' => 'chi', 'CARHR168120' => 'chi', 'CARHR172670' => 'chi', 'CARHR202500' => 'chi', 'CARHR211720' => 'chi', 'CARHR211990' => 'chi', 'CARHR265670' => 'chi', 'CARHR288900' => 'chi', 'CARHR292150' => 'chi', 'Carub.0001s1261' => 'cru', 'Carub.0001s1263' => 'cru', 'Carub.0001s1264' => 'cru', 'Carub.0001s1317' => 'cru', 'Carub.0001s1342' => 'cru', 'Carub.0001s1404' => 'cru', 'Carub.0001s1453' => 'cru', 'Carub.0001s2401' => 'cru', 'Carub.0001s2993' => 'cru', 'Carub.0001s3170' => 'cru', 'Carub.0002s0727' => 'cru', 'Carub.0002s1549' => 'cru', 'Carub.0002s1606' => 'cru', 'Carub.0003s2506' => 'cru', 'Carub.0005s0113' => 'cru', 'Carub.0005s0312' => 'cru', 'Carub.0005s0314' => 'cru', 'Carub.0005s0329' => 'cru', 'Carub.0005s0968' => 'cru', 'Carub.0005s2405' => 'cru', 'Carub.0005s2408' => 'cru', 'Carub.0006s0880' => 'cru', 'Carub.0006s1692' => 'cru', 'Carub.0007s0741' => 'cru', 'Carub.0008s0923' => 'cru', 'Carub.0345s0001' => 'cru', 'Sp1g27610' => 'spa', 'Sp1g28940' => 'spa', 'Sp1g28950' => 'spa', 'Sp1g29020' => 'spa', 'Sp2g14700' => 'spa', 'Sp6g09040' => 'spa', 'SpUn0138_0020' => 'spa', 'THA.LOC104805835' => 'tha', 'Thecc.05G284400' => 'tca', 'Thhalv10000283m.g' => 'esa', 'Thhalv10002950m.g' => 'esa', 'Thhalv10003053m.g' => 'esa', 'Thhalv10005403m.g' => 'esa', 'Thhalv10005596m.g' => 'esa', 'Thhalv10005640m.g' => 'esa', 'Thhalv10005659m.g' => 'esa', 'Thhalv10005704m.g' => 'esa', 'Thhalv10006448m.g' => 'esa', 'Thhalv10006469m.g' => 'esa', 'Thhalv10007816m.g' => 'esa', 'Thhalv10007821m.g' => 'esa', 'Thhalv10009448m.g' => 'esa', 'Thhalv10009459m.g' => 'esa', 'Thhalv10009591m.g' => 'esa', 'Thhalv10009680m.g' => 'esa', 'Thhalv10009780m.g' => 'esa', 'Thhalv10009811m.g' => 'esa', 'Thhalv10009873m.g' => 'esa', 'Thhalv10010027m.g' => 'esa', 'Thhalv10011073m.g' => 'esa', 'Thhalv10012265m.g' => 'esa', 'Thhalv10016004m.g' => 'esa', 'Thhalv10017550m.g' => 'esa', 'Thhalv10017844m.g' => 'esa', 'Thhalv10021927m.g' => 'esa', 'Thhalv10021998m.g' => 'esa', 'Thhalv10022335m.g' => 'esa', 'Thhalv10023120m.g' => 'esa', 'Thhalv10026946m.g' => 'esa', 'Thhalv10028258m.g' => 'esa', 'Thhalv10028312m.g' => 'esa' ) $gf_id = 'HOM05D001738' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001738' ) $data_identifier = 'HOM05D001738' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 74, 'aar' => (int) 15, 'aly' => (int) 33, 'ath' => (int) 16, 'bca' => (int) 64, 'bol' => (int) 41, 'bra' => (int) 32, 'chi' => (int) 31, 'cru' => (int) 26, 'spa' => (int) 7, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 32 ) $gf_gene_species = 'esa' $gf_gene_id = 'Thhalv10028312m.g' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1