Solving large scale phylogenetic problems using DCM2.

D. H. Huson, L. Vawter, Tandy Warnow

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

In an earlier paper, we described a new method for phylogenetic tree reconstruction called the Disk Covering Method, or DCM. This is a general method which can be used with any existing phylogenetic method in order to improve its performance. We showed analytically and experimentally that when DCM is used in conjunction with polynomial time distance-based methods, it improves the accuracy of the trees reconstructed. In this paper, we discuss a variant on DCM, that we call DCM2. DCM2 is designed to be used with phylogenetic methods whose objective is the solution of NP-hard optimization problems. We show that DCM2 can be used to accelerate searches for Maximum Parsimony trees. We also motivate the need for solutions to NP-hard optimization problems by showing that on some very large and important datasets, the most popular (and presumably best performing) polynomial time distance methods have poor accuracy.

Original languageEnglish
Title of host publicationProceedings / . International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology
Pages118-129
Number of pages12
StatePublished - Dec 1 1999
Externally publishedYes

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    Huson, D. H., Vawter, L., & Warnow, T. (1999). Solving large scale phylogenetic problems using DCM2. In Proceedings / . International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology (pp. 118-129)