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DeepCoalCount_tree {species_tree_ident1 [, species_tree_ident2...]} {(gene_tree_ident1 [, gene_tree_ident2...]}) [-u] [-b threshold] [-a taxa map] [result output fileresultOutputFile]
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species_tree_ident1 [, species_tree_ident2...] | Comma delimited set of species tree identifiers. | mandatory |
gene_tree_ident1 [, gene_tree_ident2...] | Comma delimited set list of gene tree identifiers. See details. | mandatory |
-u | Gene trees should be treated as unrooted. | optional |
-b threshold | Gene tree bootstrap threshold. Edges in the gene trees that have support lower than thresholdwill be contracted. | optional |
-a taxa map | Gene tree / species tree taxa association. | optional |
result output fileresultOutputFile | Optional file destination for command output. | optional |
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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_Tree {speceiesTree} {(geneTree1, geneTree2, geneTree3}); END; |
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#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_tree {speciesTree} {(geneTree1, geneTree2, geneTree3}) -u -b .5 -a <x:a; y:b; w:c; m:d; n:e>;
END;
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Command References
- C. Than and L. Nakhleh. Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5(9):e1000501, 2009.
Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phylogeny inference." Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI 6577, 531-545, 2011.
Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles." Journal of Computational Biology, 18(11): 1-18, 2011.