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
PruningBootstrapping (finance)BiologyTable (database)Computer scienceWeb serverInferenceAlgorithmData miningTheoretical computer scienceThe InternetArtificial intelligenceMathematics
Affiliated Institutions
Related Publications
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasona...
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constr...
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
Abstract Motivation: Maximum likelihood (ML) methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress...
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists o...
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood
We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under th...
Publication Info
- Year
- 2015
- Type
- article
- Volume
- 32
- Issue
- 10
- Pages
- 2798-2800
- Citations
- 1619
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
1619
OpenAlex
Cite This
Vincent Lefort,
Richard Desper,
Olivier Gascuel
(2015).
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1..
Molecular Biology and Evolution
, 32
(10)
, 2798-2800.
https://doi.org/10.1093/molbev/msv150
Identifiers
- DOI
- 10.1093/molbev/msv150