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A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance

  • Robert S. Boyer
  • Warren A. HuntJr
  • Serita M. Nelesen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

Abstract

Phylogenetic tree searching algorithms often produce thousands of trees which biologists save in Newick format in order to perform further analysis. Unfortunately, Newick is neither space efficient, nor conducive to post-tree analysis such as consensus. We propose a new format for storing phylogenetic trees that significantly reduces storage requirements while continuing to allow the trees to be used as input to post-tree analysis. We implemented mechanisms to read and write such data from and to files, and also implemented a consensus algorithm that is faster by an order of magnitude than standard phylogenetic analysis tools. We demonstrate our results on a collection of data files produced from both maximum parsimony tree searches and Bayesian methods.

Keywords

Consensus Tree Storage Requirement Input Tree Consensus Algorithm Majority Consensus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Robert S. Boyer
    • 1
  • Warren A. HuntJr
    • 1
  • Serita M. Nelesen
    • 1
  1. 1.Department of Computer SciencesThe University of TexasAustinUSA

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