Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

Paper

• If you use FastME, please cite:
  
  "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.

Related papers

• "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
• "Neighbor-Joining Revealed."
  Gascuel O., Steel M.
  Molecular Biology and Evolution. 2006 23(11):1997-2000.

References

• "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.
• "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.

Contacts

• Richard Desper (author)
  NCBI, Bethesda, USA.
• Olivier Gascuel (author)
  LIRMM, Montpellier, France.