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2004
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On contract-and-refine transformations between phylogenetic trees

10 years 2 months ago
On contract-and-refine transformations between phylogenetic trees
The inference of evolutionary trees using approaches which attempt to solve the maximum parsimony (MP) and maximum likelihood (ML) optimization problems is a standard part of much of biological data analysis. However, both problems are hard to solve: MP provably NP-hard, and ML even harder in practice. Consequently, hill-climbing heuristics are used to analyze datasets for phylogeny reconstruction. Two primary topological transformations have been used in the most popular heuristics: TBR (treebisection-and-reconnection) and ECR (edge-contractionsand-refinements). While most of the popular heuristics exclusively use TBR moves to explore tree space, some recent methods have used ECR in conjunction with TBR and found significant improvements in the speed and accuracy with which they can analyze datasets. In this paper we analyze ECR moves in detail, and provide results on the diameter of the tree space, the neigborhood intersection with TBR, structural analysis of the ECR operation, and ...
Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy
Added 31 Oct 2010
Updated 31 Oct 2010
Type Conference
Year 2004
Where SODA
Authors Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy Warnow
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