...
| Code Block | ||
|---|---|---|
| ||
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="f86d5308-31e1-4e46-902c-0a3ef38ec10e"><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="eff2bed1-b432-4a8b-8dba-65ce5d1e833d"><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 |
...
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
| Code Block | ||
|---|---|---|
| ||
#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;
|
...