Extensions and improvements to the chordal graph approach to the multi-state perfect phylogeny problem

Authors:
Rob Gysel;Dan Gusfield
Affiliations:
Department of Computer Science, University of California, Davis, Davis, CA;Department of Computer Science, University of California, Davis, Davis, CA
Venue:
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Year:
2010

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Abstract

The multi-state perfect phylogeny problem is a classic problem in computational biology. When no perfect phylogeny exists, it is of interest to find a set of characters to remove in order to obtain a perfect phylogeny in the remaining data. This is known as the character removal problem. We show how to use chordal graphs and triangulations to solve the character removal problem for an arbitrary number of states, which was previously unsolved. We outline a preprocessing technique that speeds up the computation of the minimal separators of a graph. Minimal separators are used in our solution to the missing data character removal problem and to the solution of the perfect phylogeny problem with missing data discussed in [10].