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.

User report

0 user reviews

0 user reviews

No review has been posted.

FastTree forum

No open topic.

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).

Related Phylogenetic inference tools

Most Recent Tools

Desktop app
TreeTime TreeTime

TreeTime

Provides routines for ancestral sequence reconstruction and the inference of…

Provides routines for ancestral sequence reconstruction and the inference of molecular-clock phylogenies. TreeTime is a Markov chain Monte Carlo (MCMC) framework for Bayesian phylogeny…

Desktop app
phyloSkeleton phyloSkeleton

phyloSkeleton

Selects the most representative organisms, following a set of simple rules…

Selects the most representative organisms, following a set of simple rules based on taxonomy and assembly quality. phyloSkeleton allows users to retrieve the genomes from public databases (NCBI,…

Web app
Desktop app
System for Integrate… System for Integrate Genomic Resources and…

STINGRAY System for Integrate Genomic Resources and Analyses

Offers a complete annotation pipeline for integrating, analyzing, annotating…

Offers a complete annotation pipeline for integrating, analyzing, annotating and presenting genomic and expression data from sequencing platforms. STINGRAY offers to user a phylogenetic module that…

Desktop app
sampled-ancestors sampled-ancestors

sampled-ancestors

Infers trees in which sampled individuals can be direct ancestors of other…

Infers trees in which sampled individuals can be direct ancestors of other sampled individuals. This method allows the detection of sampled ancestors as well as the estimation of the probability that…

Most Popular Tools

PhyloPat PhyloPat

PhyloPat

Allows the complete Ensembl gene database to be queried using phylogenetic…

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.