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FastME

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NGS

FastME 2.0: a comprehensive, accurate and fast distance-based phylogeny inference program.

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange (NNI). The new 2.0 version also includes Subtree Pruning and Regrafting (SPR), while remaining as fast as NJ and providing a number of facilities: distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations.

FastME is now available on GitLab.

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Supplementary material (FastME 2.0 paper, submitted)

Download an archive (.zip) containing:

• 20 input alignments used to compare distance methods (NJ, NJ+OLSME, BioNJ, NJ+NNI, NJ+SPR, NJ+SPR-Γ, FastTree1)
• 140 inferred trees and corresponding log-likelihoods
• 1 resuming sheet (.xls and .ods)

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FastME papers

• "FastME 2.0: a comprehensive, accurate and fast distance-based phylogeny inference program."
  Lefort V., Desper R., Gascuel O.
  Molecular Biology and Evolution, 2015.
• "Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle."
  Desper R., Gascuel O.
  Journal of Computational Biology. 2002 9(5):687-705.
• "Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting."
  Desper R., Gascuel O.
  Molecular Biology and Evolution. 2004 21(3):587-598.
• "Getting a Tree Fast: Neighbor Joining, FastME, and Distance-Based Methods."
  Desper R., Gascuel O.
  Current Protocols in Bioinformatics. 2006 6.3.1-6.3.28.
  Editied by John Wiley & Sons

Related papers & references

• "Neighbor-Joining Revealed."
  Gascuel O., Steel M.
  Molecular Biology and Evolution. 2006 23(11):1997-2000.
• "Shortest triplet clustering: reconstructing large phylogenies using representative sets."
  Vinh le S., von Haeseler A.
  BMC Bioinformatics. 2005 8;6:92.
  "We found that balanced_NNI boosts the topological accuracy of all methods including STC [author's method]".
• "BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data."
  Gascuel O.
  Molecular Biology and Evolution. 1997 14(7):685-695.
  Please cite this paper when using BIONJ option in FastME.
• "Concerning the NJ algorithm and its unweighted version, UNJ."
  Gascuel O.
  Pp. 149-170 in Mathematical Hierarchies and Biology (B. Mirkin, F.R. McMorris, F.S. Roberts and A. Rzhetsky, eds.), 1997
  DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Amer. Math. Soc., Providence, RI.
  Please cite this paper when using BIONJ option in FastME.
• "The neighbor-joining method: a new method for reconstructing phylogenetic trees."
  Saitou N., Nei M.
  Molecular Biology and Evolution. 1987 4(4):406-25.
  Please cite this paper when using NJ option in FastME.

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Contacts

• Olivier Gascuel
  LIRMM, Montpellier, France.
• Vincent Lefort
  LIRMM, Montpellier, France.

Contact: Vincent Lefort, LIRMM.