Statistically based postprocessing of phylogenetic analysis by clustering

Bioinformatics. 2002;18 Suppl 1:S285-93. doi: 10.1093/bioinformatics/18.suppl_1.s285.

Abstract

Motivation: Phylogenetic analyses often produce thousands of candidate trees. Biologists resolve the conflict by computing the consensus of these trees. Single-tree consensus as postprocessing methods can be unsatisfactory due to their inherent limitations.

Results: In this paper we present an alternative approach by using clustering algorithms on the set of candidate trees. We propose bicriterion problems, in particular using the concept of information loss, and new consensus trees called characteristic trees that minimize the information loss. Our empirical study using four biological datasets shows that our approach provides a significant improvement in the information content, while adding only a small amount of complexity. Furthermore, the consensus trees we obtain for each of our large clusters are more resolved than the single-tree consensus trees. We also provide some initial progress on theoretical questions that arise in this context.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Validation Study

MeSH terms

  • Algorithms*
  • Cluster Analysis*
  • Consensus Sequence / genetics
  • Evolution, Molecular*
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation / genetics*
  • Models, Genetic*
  • Models, Statistical
  • Phylogeny*
  • Sequence Analysis / methods