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

Vincent Lefort (1, 2) , Richard Desper (1, 2) , Olivier Gascuel (2)

1 IBC - Institut de Biologie Computationnelle
2 MAB - Méthodes et Algorithmes pour la Bioinformatique

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/).

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

Domaines: Bio-informatique [q-bio.QM]

Vincent Lefort, Richard Desper, Olivier Gascuel. FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program. Molecular Biology and Evolution, 2015, 32 (10), pp.2798-2800. ⟨10.1093/molbev/msv150⟩. ⟨lirmm-01283927⟩