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

Lefort V., Desper R., Gascuel O.

Molecular Biology and Evolution 32(10), 2798-800, 2015.

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
Algorithm

Tree Refinement
Tree refinement with NNI		NNI_BalME (Best of NNI & SPR)	NNI_OLS
Tree refinement with SPR		SPR_BalME (Best of NNI & SPR)

Branch length estimation
Select the branch length type to assign to the topology (only available for user starting topology)	BalLS	OLS

Branch support
Perform bootstrap		yes	no

Name of your analysis
Your email
Please confirm your email