FastME 2.0: a comprehensive, accurate and fast distance-based phylogeny inference program.

Lefort V., Desper R., Gascuel O.

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange (NNI). The new 2.0 version also includes Subtree Pruning and Regrafting (SPR), 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 now available on GitLab.

FastME online execution

Input Data
Input data (PHYLIP format) User input file Matrix example file DNA example file
Data Type (PHYLIP format)
Number of data sets

Substitution Model
Substitution model
Gamma distributed rates across sites yes no
Gamma shape parameter

Tree Building
Use starting topology(s) (Newick format) yes no

Branch support
Perform bootstrap yes no

Name of your analysis
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