CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2010 vol.7 Issue No.01 - January-March
Issue No.01 - January-March (2010 vol.7)
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
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.
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.2008.13