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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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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.
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