Online

Constructs large phylogenies and estimates their reliability. FastTree uses nearest-neighbor interchanges (NNIs), the minimum-evolution criterion, minimum-evolution subtree-pruning-regrafting (SPRs) and maximumlikelihood NNIs to improve the tree. It uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

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FastTree versioning

No versioning.

FastTree classification

FastTree specifications

Software type:
Package
Restrictions to use:
None
Output format:
NEWICK
Programming languages:
C
Version:
2.1.9
Interface:
Command line interface
Input format:
FASTA, PHYLIP
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://microbesonline.org/fasttree/FastTree.c

Publications

  • (Price et al., 2010) FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One.
    PMID: 20224823
  • (Price et al., 2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol.
    PMID: 19377059

FastTree support

Documentation

Credits

Institution(s)

Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA; Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Lab, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA

Funding source(s)

This work was supported by a grant from the US Department of Energy Genomics: GTL program (DE-AC02-05CH11231).

Link to literature

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