Approximate Maximum Parsimony and Ancestral Maximum Likelihood

Authors:
Noga Alon;Benny Chor;Fabio Pardi;Anat Rapoport
Affiliations:
Tel Aviv University, Tel Aviv;Tel Aviv University, Tel Aviv;EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge;Tel Aviv University, Tel Aviv
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2010

Citing 4
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Shrinkage Effect in Ancestral Maximum Likelihood

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Abstract

We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.