Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Oct;32(10):2798-800.
doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Vincent Lefort  1 , Richard Desper  1 , Olivier Gascuel  2
Affiliations

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Vincent Lefort et al. Mol Biol Evol. 2015 Oct.

Abstract

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, 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 available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).

Keywords: (balanced) minimum evolution; NNI and SPR topological moves; distance-based; fast algorithms; phylogeny inference.

PubMed Disclaimer

References

    1. Desper R, Gascuel O. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comp Biol. 9:687–705. - PubMed
    1. Desper R, Gascuel O. 2004. Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol. 21:587-598. - PubMed
    1. Gascuel O, Steel M. 2006. Neighbor-joining revealed. Mol Biol Evol. 23:1997–2000. - PubMed
    1. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321. - PubMed
    1. Kuhner MK, Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 11:459-468. - PubMed

Publication types