title: FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.
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/).
authors.affiliation: Institut de Biologie Computationnelle, LIRMM, UMR 5506: CNRS & Université de Montpellier, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lefort
authors.affiliation: Institut de Biologie Computationnelle, LIRMM, UMR 5506: CNRS & Université de Montpellier, France.
authors.forename: Richard
authors.initials: R
authors.lastname: Desper
authors.affiliation: Institut de Biologie Computationnelle, LIRMM, UMR 5506: CNRS & Université de Montpellier, France gascuel@lirmm.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Gascuel
mesh_terms: D000465:Algorithms; D008962:Models, Theoretical; D010802:Phylogeny
keywords: (balanced) minimum evolution; NNI and SPR topological moves; distance-based; fast algorithms; phylogeny inference