An improved algorithm for the macro-evolutionary phylogeny problem

Authors:
Behshad Behzadi;Martin Vingron
Affiliations:
Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany;Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin, Germany
Venue:
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Year:
2006

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Abstract

Macro-evolutionary processes (e.g., gene duplication and loss) have rarely been incorporated into gene phylogeny reconstruction methods. Durand et al. [5] have proposed a polynomial time dynamic programming algorithm to find the gene family tree that optimizes a macro-evolutionary criterion which is the weighted sum of the number of gene duplications and losses. The complexity of this algorithm is O(nm2) where n is the number of species and m is the maximum number of copies of the gene in a species. In this paper, we propose an improved algorithm with time complexity of O(nm) for solving this problem. We also show, that the problem can be solved in O(n) if unit costs are considered for both loss and duplication.