Molecular Biology and Evolution · 2015 · 1.8K citations · 11 references
Life SciencesBioinformaticsEvolutionary BiologyComputational BiologyMolecular EvolutionPhylogeneticsDistance-based PhylogeneticsMolecular PhylogenyPhylogenetic AnalysisPhylogenetic Tree ReconstructionTree Topology ComparisonDistance EstimationDistance-based PhylogenyFastmeMinimum EvolutionNeighbor-joiningNeighbor-joining AnalysisPhylogenetic Tree Topology InferencePruning
FastME is based on balanced minimum evolution, the principle underlying Neighbor Joining. FastME offers distance‑based algorithms for phylogeny inference. FastME 2.0 extends the original by adding Subtree Pruning and Regrafting, supports diverse distance models, bootstrapping, parallel runs, and is accessible via command line, PHYLIP‑style, and a web interface. FastME outperforms Neighbor Joining by executing efficient topological moves.
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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