CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010 vol.7 Issue No.01 - January-March

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Issue No.01 - January-March (2010 vol.7)

pp: 183-187

Noga Alon , Tel Aviv University, Tel Aviv

Benny Chor , Tel Aviv University, Tel Aviv

Fabio Pardi , EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge

Anat Rapoport , Tel Aviv University, Tel Aviv

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.13

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.

INDEX TERMS

Phylogenetic reconstruction, ancestral maximum likelihood, maximum parsimony, Steiner trees, approximation algorithms.

CITATION

Noga Alon, Benny Chor, Fabio Pardi, Anat Rapoport, "Approximate Maximum Parsimony and Ancestral Maximum Likelihood",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.7, no. 1, pp. 183-187, January-March 2010, doi:10.1109/TCBB.2008.13REFERENCES