The role of diverse populations in phylogenetic analysis

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The role of diverse populations in phylogenetic analysis
The most popular approaches for reconstructing phylogenetic trees attempt to solve NP-hard optimization criteria such as maximum parsimony (MP). Currently, the bestperforming heuristic for reconstructing MP trees is RecursiveIterative DCM3 (Rec-I-DCM3), which uses a single tree (or solution) to guide its way through an exponentially-sized tree space. To improve performance further, we designed Cooperative Rec-I-DCM3, a population-based approach for utilizing a population of Rec-I-DCM3 trees. We compare the performance of Cooperative Rec-I-DCM3 to Rec-I-DCM3 on four large biological datasets. Of particular interest is Cooperative Rec-I-DCM3's selection criteria for maintaining a population of solutions. Our experiments reveal that diverse populations outperform Rec-I-DCM3 in terms of average rates of convergence to best-known MP scores. To achieve greater performance, we designed an elitist population strategy, in which each solution's tree score matches that of the best scor...
Tiffani L. Williams, Marc L. Smith
Added 23 Aug 2010
Updated 23 Aug 2010
Type Conference
Year 2006
Authors Tiffani L. Williams, Marc L. Smith
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