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 Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Neare...

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Bibliographic Details
Published in:Molecular biology and evolution Vol. 32; no. 10; pp. 2798 - 2800
Main Authors: Lefort, Vincent, Desper, Richard, Gascuel, Olivier
Format: Journal Article
Language:English
Published: United States Oxford University Press 01.10.2015
Oxford University Press (OUP)
Subjects:
Algorithms
Bioinformatics
Computer Science
Deoxyribonucleic acid
DNA
Evolutionary biology
Models, Theoretical
Phylogenetics
Phylogeny
Proteins
Resources
NNI and SPR topological moves
phylogeny inference
distance-based
fast algorithms
(balanced) minimum evolution
ISSN:0737-4038, 1537-1719, 1537-1719
Online Access:Get full text
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Summary: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/).
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Associate editor: Michael Rosenberg
ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/msv150