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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 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'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 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'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 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' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ), 'gf_id' => 'HOM05D001963', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001963' ), 'data_identifier' => 'HOM05D001963', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001963', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '337', 'num_species' => '4' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'ClCG03G006670' => 'cla', 'ClCG03G009190' => 'cla', 'ClCG04G001600' => 'cla', 'ClCG07G006680' => 'cla', 'ClCG07G007590' => 'cla', 'ClCG11G010140' => 'cla', 'CsaV3_2G013860' => 'csa', 'CsaV3_2G017350' => 'csa', 'CsaV3_5G010700' => 'csa', 'CsaV3_6G034360' => 'csa', 'MELO3C003796.2' => 'cme', 'MELO3C008456.2' => 'cme', 'MELO3C020227.2' => 'cme', 'MELO3C020937.2' => 'cme', 'MELO3C022907.2' => 'cme', 'MELO3C027100.2' => 'cme', 'MELO3C027560.2' => 'cme', 'MELO3C027610.2' => 'cme', 'MELO3C027624.2' => 'cme', 'MELO3C027653.2' => 'cme', 'MELO3C027661.2' => 'cme', 'MELO3C027728.2' => 'cme', 'MELO3C027729.2' => 'cme', 'MELO3C027772.2' => 'cme', 'MELO3C027775.2' => 'cme', 'MELO3C027791.2' => 'cme', 'MELO3C027809.2' => 'cme', 'MELO3C027817.2' => 'cme', 'MELO3C027871.2' => 'cme', 'MELO3C027878.2' => 'cme', 'MELO3C027880.2' => 'cme', 'MELO3C027890.2' => 'cme', 'MELO3C027924.2' => 'cme', 'MELO3C027970.2' => 'cme', 'MELO3C027985.2' => 'cme', 'MELO3C028034.2' => 'cme', 'MELO3C028086.2' => 'cme', 'MELO3C028156.2' => 'cme', 'MELO3C028216.2' => 'cme', 'MELO3C028235.2' => 'cme', 'MELO3C028240.2' => 'cme', 'MELO3C028250.2' => 'cme', 'MELO3C028253.2' => 'cme', 'MELO3C028369.2' => 'cme', 'MELO3C028413.2' => 'cme', 'MELO3C028427.2' => 'cme', 'MELO3C028430.2' => 'cme', 'MELO3C028440.2' => 'cme', 'MELO3C028447.2' => 'cme', 'MELO3C028459.2' => 'cme', 'MELO3C028460.2' => 'cme', 'MELO3C028470.2' => 'cme', 'MELO3C028474.2' => 'cme', 'MELO3C028480.2' => 'cme', 'MELO3C028487.2' => 'cme', 'MELO3C028497.2' => 'cme', 'MELO3C028545.2' => 'cme', 'MELO3C028550.2' => 'cme', 'MELO3C028551.2' => 'cme', 'MELO3C028563.2' => 'cme', 'MELO3C028667.2' => 'cme', 'MELO3C028710.2' => 'cme', 'MELO3C028780.2' => 'cme', 'MELO3C028794.2' => 'cme', 'MELO3C028799.2' => 'cme', 'MELO3C028813.2' => 'cme', 'MELO3C028826.2' => 'cme', 'MELO3C028832.2' => 'cme', 'MELO3C028854.2' => 'cme', 'MELO3C028855.2' => 'cme', 'MELO3C028900.2' => 'cme', 'MELO3C028901.2' => 'cme', 'MELO3C028920.2' => 'cme', 'MELO3C028925.2' => 'cme', 'MELO3C028952.2' => 'cme', 'MELO3C028968.2' => 'cme', 'MELO3C028977.2' => 'cme', 'MELO3C028986.2' => 'cme', 'MELO3C028992.2' => 'cme', 'MELO3C029025.2' => 'cme', 'MELO3C029029.2' => 'cme', 'MELO3C029043.2' => 'cme', 'MELO3C029052.2' => 'cme', 'MELO3C029062.2' => 'cme', 'MELO3C029063.2' => 'cme', 'MELO3C029099.2' => 'cme', 'MELO3C029168.2' => 'cme', 'MELO3C029190.2' => 'cme', 'MELO3C029216.2' => 'cme', 'MELO3C029231.2' => 'cme', 'MELO3C029232.2' => 'cme', 'MELO3C029233.2' => 'cme', 'MELO3C029234.2' => 'cme', 'MELO3C029544.2' => 'cme', 'MELO3C029550.2' => 'cme', 'MELO3C029551.2' => 'cme', 'MELO3C029617.2' => 'cme', 'MELO3C029618.2' => 'cme', 'MELO3C029644.2' => 'cme', 'MELO3C029647.2' => 'cme', 'MELO3C029673.2' => 'cme', 'MELO3C029679.2' => 'cme', 'MELO3C029696.2' => 'cme', 'MELO3C029715.2' => 'cme', 'MELO3C029842.2' => 'cme', 'MELO3C029861.2' => 'cme', 'MELO3C029870.2' => 'cme', 'MELO3C029878.2' => 'cme', 'MELO3C029911.2' => 'cme', 'MELO3C029975.2' => 'cme', 'MELO3C029985.2' => 'cme', 'MELO3C029986.2' => 'cme', 'MELO3C030089.2' => 'cme', 'MELO3C030136.2' => 'cme', 'MELO3C030142.2' => 'cme', 'MELO3C030160.2' => 'cme', 'MELO3C030170.2' => 'cme', 'MELO3C030180.2' => 'cme', 'MELO3C030188.2' => 'cme', 'MELO3C030195.2' => 'cme', 'MELO3C030197.2' => 'cme', 'MELO3C030200.2' => 'cme', 'MELO3C030230.2' => 'cme', 'MELO3C030231.2' => 'cme', 'MELO3C030235.2' => 'cme', 'MELO3C030273.2' => 'cme', 'MELO3C030283.2' => 'cme', 'MELO3C030419.2' => 'cme', 'MELO3C030431.2' => 'cme', 'MELO3C030432.2' => 'cme', 'MELO3C030566.2' => 'cme', 'MELO3C030572.2' => 'cme', 'MELO3C030642.2' => 'cme', 'MELO3C030645.2' => 'cme', 'MELO3C030735.2' => 'cme', 'MELO3C030777.2' => 'cme', 'MELO3C030802.2' => 'cme', 'MELO3C030803.2' => 'cme', 'MELO3C030815.2' => 'cme', 'MELO3C030831.2' => 'cme', 'MELO3C030855.2' => 'cme', 'MELO3C030873.2' => 'cme', 'MELO3C030896.2' => 'cme', 'MELO3C030912.2' => 'cme', 'MELO3C030919.2' => 'cme', 'MELO3C030925.2' => 'cme', 'MELO3C030972.2' => 'cme', 'MELO3C031006.2' => 'cme', 'MELO3C031127.2' => 'cme', 'MELO3C031163.2' => 'cme', 'MELO3C031311.2' => 'cme', 'MELO3C031334.2' => 'cme', 'MELO3C031357.2' => 'cme', 'MELO3C031389.2' => 'cme', 'MELO3C031390.2' => 'cme', 'MELO3C031402.2' => 'cme', 'MELO3C031432.2' => 'cme', 'MELO3C031439.2' => 'cme', 'MELO3C031441.2' => 'cme', 'MELO3C031469.2' => 'cme', 'MELO3C031482.2' => 'cme', 'MELO3C031488.2' => 'cme', 'MELO3C031492.2' => 'cme', 'MELO3C031540.2' => 'cme', 'MELO3C031765.2' => 'cme', 'MELO3C031804.2' => 'cme', 'MELO3C031923.2' => 'cme', 'MELO3C031939.2' => 'cme', 'MELO3C031940.2' => 'cme', 'MELO3C031949.2' => 'cme', 'MELO3C031952.2' => 'cme', 'MELO3C031957.2' => 'cme', 'MELO3C031958.2' => 'cme', 'MELO3C031959.2' => 'cme', 'MELO3C031977.2' => 'cme', 'MELO3C031998.2' => 'cme', 'MELO3C032003.2' => 'cme', 'MELO3C032005.2' => 'cme', 'MELO3C032009.2' => 'cme', 'MELO3C032027.2' => 'cme', 'MELO3C032028.2' => 'cme', 'MELO3C032049.2' => 'cme', 'MELO3C032090.2' => 'cme', 'MELO3C032099.2' => 'cme', 'MELO3C032137.2' => 'cme', 'MELO3C032140.2' => 'cme', 'MELO3C032141.2' => 'cme', 'MELO3C032150.2' => 'cme', 'MELO3C032171.2' => 'cme', 'MELO3C032181.2' => 'cme', 'MELO3C032190.2' => 'cme', 'MELO3C032198.2' => 'cme', 'MELO3C032226.2' => 'cme', 'MELO3C032234.2' => 'cme', 'MELO3C032245.2' => 'cme', 'MELO3C032266.2' => 'cme', 'MELO3C032421.2' => 'cme', 'MELO3C032439.2' => 'cme', 'MELO3C032440.2' => 'cme', 'MELO3C032546.2' => 'cme', 'MELO3C032579.2' => 'cme', 'MELO3C032669.2' => 'cme', 'MELO3C032694.2' => 'cme', 'MELO3C032701.2' => 'cme', 'MELO3C032712.2' => 'cme', 'MELO3C032735.2' => 'cme', 'MELO3C032745.2' => 'cme', 'MELO3C032748.2' => 'cme', 'MELO3C032749.2' => 'cme', 'MELO3C032752.2' => 'cme', 'MELO3C032774.2' => 'cme', 'MELO3C032780.2' => 'cme', 'MELO3C032793.2' => 'cme', 'MELO3C032794.2' => 'cme', 'MELO3C032812.2' => 'cme', 'MELO3C033043.2' => 'cme', 'MELO3C033126.2' => 'cme', 'MELO3C033127.2' => 'cme', 'MELO3C033217.2' => 'cme', 'MELO3C033222.2' => 'cme', 'MELO3C033223.2' => 'cme', 'MELO3C033228.2' => 'cme', 'MELO3C033252.2' => 'cme', 'MELO3C033253.2' => 'cme', 'MELO3C033282.2' => 'cme', 'MELO3C033301.2' => 'cme', 'MELO3C033302.2' => 'cme', 'MELO3C033337.2' => 'cme', 'MELO3C033354.2' => 'cme', 'MELO3C033357.2' => 'cme', 'MELO3C033376.2' => 'cme', 'MELO3C033397.2' => 'cme', 'MELO3C033430.2' => 'cme', 'MELO3C033432.2' => 'cme', 'MELO3C033433.2' => 'cme', 'MELO3C033435.2' => 'cme', 'MELO3C033436.2' => 'cme', 'MELO3C033453.2' => 'cme', 'MELO3C033468.2' => 'cme', 'MELO3C033477.2' => 'cme', 'MELO3C033483.2' => 'cme', 'MELO3C033486.2' => 'cme', 'MELO3C033491.2' => 'cme', 'MELO3C033515.2' => 'cme', 'MELO3C033602.2' => 'cme', 'MELO3C033633.2' => 'cme', 'MELO3C033640.2' => 'cme', 'MELO3C033641.2' => 'cme', 'MELO3C033661.2' => 'cme', 'MELO3C033679.2' => 'cme', 'MELO3C033707.2' => 'cme', 'MELO3C033710.2' => 'cme', 'MELO3C033734.2' => 'cme', 'MELO3C033748.2' => 'cme', 'MELO3C033814.2' => 'cme', 'MELO3C033850.2' => 'cme', 'MELO3C033852.2' => 'cme', 'MELO3C033853.2' => 'cme', 'MELO3C033854.2' => 'cme', 'MELO3C033864.2' => 'cme', 'MELO3C033869.2' => 'cme', 'MELO3C033870.2' => 'cme', 'MELO3C033887.2' => 'cme', 'MELO3C033899.2' => 'cme', 'MELO3C033913.2' => 'cme', 'MELO3C033917.2' => 'cme', 'MELO3C033943.2' => 'cme', 'MELO3C033944.2' => 'cme', 'MELO3C033983.2' => 'cme', 'MELO3C034274.2' => 'cme', 'MELO3C034287.2' => 'cme', 'MELO3C034322.2' => 'cme', 'MELO3C034326.2' => 'cme', 'MELO3C034327.2' => 'cme', 'MELO3C034339.2' => 'cme', 'MELO3C034349.2' => 'cme', 'MELO3C034360.2' => 'cme', 'MELO3C034375.2' => 'cme', 'MELO3C034393.2' => 'cme', 'MELO3C034430.2' => 'cme', 'MELO3C034431.2' => 'cme', 'MELO3C034435.2' => 'cme', 'MELO3C034455.2' => 'cme', 'MELO3C034470.2' => 'cme', 'MELO3C034489.2' => 'cme', 'MELO3C034509.2' => 'cme', 'MELO3C034528.2' => 'cme', 'MELO3C034536.2' => 'cme', 'MELO3C034584.2' => 'cme', 'MELO3C034747.2' => 'cme', 'MELO3C034759.2' => 'cme', 'MELO3C034760.2' => 'cme', 'MELO3C034765.2' => 'cme', 'MELO3C034784.2' => 'cme', 'MELO3C034837.2' => 'cme', 'MELO3C034846.2' => 'cme', 'MELO3C034892.2' => 'cme', 'MELO3C034939.2' => 'cme', 'MELO3C034953.2' => 'cme', 'MELO3C034958.2' => 'cme', 'MELO3C034979.2' => 'cme', 'MELO3C034992.2' => 'cme', 'MELO3C035008.2' => 'cme', 'MELO3C035011.2' => 'cme', 'MELO3C035017.2' => 'cme', 'MELO3C035037.2' => 'cme', 'MELO3C035061.2' => 'cme', 'MELO3C035092.2' => 'cme', 'MELO3C035108.2' => 'cme', 'MELO3C035123.2' => 'cme', 'MELO3C035130.2' => 'cme', 'MELO3C035134.2' => 'cme', 'MELO3C035149.2' => 'cme', 'MELO3C035150.2' => 'cme', 'MELO3C035152.2' => 'cme', 'MELO3C035153.2' => 'cme', 'MELO3C035156.2' => 'cme', 'MELO3C035157.2' => 'cme', 'MELO3C035258.2' => 'cme', 'MELO3C035375.2' => 'cme', 'MELO3C035385.2' => 'cme', 'MELO3C035397.2' => 'cme', 'MELO3C035458.2' => 'cme', 'MELO3C035465.2' => 'cme', 'MELO3C035485.2' => 'cme', 'MELO3C035493.2' => 'cme', 'MELO3C035533.2' => 'cme', 'MELO3C035534.2' => 'cme', 'MELO3C035539.2' => 'cme', 'MELO3C035560.2' => 'cme', 'MELO3C035577.2' => 'cme', 'MELO3C035587.2' => 'cme', 'MELO3C035623.2' => 'cme', 'MELO3C035653.2' => 'cme', 'MELO3C035657.2' => 'cme', 'MELO3C035688.2' => 'cme', 'Sed0001751' => 'sed' ) $gf_id = 'HOM05D001963' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001963' ) $data_identifier = 'HOM05D001963' $data_type = 'gf_id' $species_gene_counts = array( 'cla' => (int) 6, 'csa' => (int) 4, 'cme' => (int) 326, 'sed' => (int) 1 ) $gf_gene_species = 'sed' $gf_gene_id = 'Sed0001751' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0