Issue No. 01 - January-March (2010 vol. 7)
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.13
Fabio Pardi , EMBL-European Bioinformatics Institute and University of Cambridge, Cambridge
Noga Alon , Tel Aviv University, Tel Aviv
Anat Rapoport , Tel Aviv University, Tel Aviv
Benny Chor , Tel Aviv University, Tel Aviv
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.
Phylogenetic reconstruction, ancestral maximum likelihood, maximum parsimony, Steiner trees, approximation algorithms.
Fabio Pardi, Noga Alon, Anat Rapoport, Benny Chor, "Approximate Maximum Parsimony and Ancestral Maximum Likelihood", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. , pp. 183-187, January-March 2010, doi:10.1109/TCBB.2008.13