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NJIT Mathematical Biology Seminar

Tuesday, March 7, 2006, 4:00 pm
Cullimore Hall 611
New Jersey Institute of Technology

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Boosting phylogeny reconstruction using Recursive-Iterative-DCM3

Usman W. Roshan

Computer Science Department
New Jersey Institute of Technology

The Disk Covering Method (DCM) family of algorithms improve an existing phylogeny reconstruction method by deploying it in a divide-and-conquer framework. DCMs divide the input set of species into smaller subsets, compute phylogenies on the subsets using the given base phylogeny reconstruction method, merge the phylogenies using the Strict Consensus Merger into a supertree, and refine the resulting supertree to make it binary. The latest and most effective DCM to date is Recursive-Iterative-DCM3 (Rec-I-DCM3) which combines the basic divide-and-conquer strategy with iteration. In this talk I will describe the Rec-I-DCM3 method and present experimental results for improving phylogeny reconstruction using MP heuristics (with PAUP* and TNT), ML heuristics (with PAUP* and RAxML), and simultaneous alignment and phylogeny reconstruction heuristics (using Poy).