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Issue No. 01 - January-March (2009 vol. 6)
ISSN: 1545-5963
pp: 97-102
Stefan Grünewald , CAS-MPG Partner Institute for Computational Biology Max Planck Institute for Mathematics in the Sciences, Shanghai Leipzig
Vincent Moulton , University of East Anglia
With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to processes such as gene duplication and lineage sorting, it is important to better understand how commonly used phylogenetic inference methods behave on such "phylogenetic mixtures". Here we shall focus on how parsimony, one of the most popular methods for reconstructing phylogenetic trees, behaves for mixtures of two trees. In particular, we show that (i) the parsimony problem is NP-complete for mixtures of two trees, (ii) there are mixtures of two trees that have exponentially many (in the number of leaves) most parsimonious trees, and (iii) give an explicit description of the most parsimonious tree(s) and scores corresponding to the mixture of a pair of trees related by a single TBR operation.
Applications, Biology and genetics

V. Moulton and S. Grünewald, "Maximum Parsimony for Tree Mixtures," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. , pp. 97-102, 2008.
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