Description
Counts the number of extra lineages contributed by a species tree and a set of gene trees. The trees must be specified in the rich newick format. Specifying more than one species three will run the command multiple times with one execution per species tree.
DeepCoalCount {species_tree_ident1 [, species_tree_ident2...]} {gene_tree_ident1 [, gene_tree_ident2...]} [-u] [-b threshold] [-a taxa map] [result output file]
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species_tree_ident1 [, species_tree_ident2...] |
Comma delimited set of species tree identifiers. |
mandatory |
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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 |
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-b threshold |
Gene tree bootstrap threshold. |
optional |
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-a taxa map |
Gene tree / species tree taxa association. |
optional |
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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.
By default, it is assumed that only one individual is sampled per species in gene trees. However, the option [-a taxa map] allows multiple alleles to be sampled.
Examples
#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;
#NEXUS
BEGIN TREES;
Tree speceiesTree = ((((x,y),w),m),n);
Tree geneTree1 = ((((a::.5,b::.5)::.5,c::.5)::.5,d::.5)::.5,e::.5)::.5;
Tree geneTree2 = ((a::.5,b::.5)::.5,((c::.5,e::.5)::.5,d::.5)::.5)::.5;
Tree geneTree3 = ((a::.5,c::.5)::.5,((b::.5,e::.5)::.5,d::.5)::.5)::.5;
END;
BEGIN PHYLONET;
DeepCoalCount {speciesTree} {geneTree1, geneTree2, geneTree3} -u -b .5 -a <x:a; y:b; w:c; m:d; n:e>;
END;