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DeepCoalCount {species_tree_ident1 [, species_tree_ident2...]} {gene_tree_ident1 [, gene_tree_ident2...]} [-u] [-b threshold] [-a taxa map] [result output file] |
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="5cae2199-5322-4eca-99ad-5b6b3ab884a4"><ac:plain-text-body><![CDATA[ | species_tree_ident1 [, species_tree_ident2...] | Comma delimited set of species tree identifiers. | mandatory | ]]></ac:plain-text-body></ac:structured-macro> | <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2aacbf89-db42-4bc0-92af-7f29d26a4044"><ac:plain-text-body><![CDATA[ |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited set of gene tree identifiers. | mandatory | |||
]]></ac:plain-text -body></ac:structured-macro> -u | Gene trees should be treated as unrooted. | optional | |||
-b threshold | Gene tree bootstrap threshold. | optional | |||
-a taxa map | Gene tree / species tree taxa association. | optional | |||
result output file | Optional file destination for command output. | optional |
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The command assumes that the trees are rooted. Gene trees may be reinterpreted as unrooted with the {{\[-u
\]
}} flag.unmigrated-wiki-markup
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option {{\[-a
[_taxa
map
_|Taxa Map Command Parameter]
\]}} allows multiple alleles to be sampled.
Examples
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#NEXUS BEGIN TREES; Tree speceiesTree = ((((a,b),c),d),e); Tree geneTree1 = ((((a,b),c),d),e); Tree geneTree2 = ((a,b),((c,e),d)); Tree geneTree3 = ((a,c),((b,e),d)); END; BEGIN PHYLONET; DeepCoalCount {speceiesTree} {geneTree1, geneTree2, geneTree3}; END; |
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