Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep

  • Authors:
  • Constantinos Daskalakis;Elchanan Mossel;Sebastien Roch

  • Affiliations:
  • Microsoft Research,;UC Berkeley and Weizman Institute,;Microsoft Research,

  • Venue:
  • RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
  • Year:
  • 2009

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Abstract

We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is guaranteed to contain all edges that are: 1) sufficiently long and 2) sufficiently close to the leaves. How much of the true tree is recovered depends on the sequence length provided. The algorithm is distance-based and runs in polynomial time.