FastTree

Description

fasttree website

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

Environment Modules

Run module spider fasttree to find out what environment modules are available for this application.

Environment Variables

• HPC_FASTTREE_DIR - installation directory
• HPC_FASTTREE_BIN - executable directory

Citation

If you publish research that uses fasttree you have to cite it as follows:

The following papers describe FastTree. The first paper describes FastTree 1.0, and the second paper describes heuristic minimum-evolution SPR moves, maximum-likelihood NNIs, and SH-like local supports. We have also eliminated the O(N2) steps in the neighbor-joining phase, and implemented maximum-likelihood NNI moves and SH-like supports (see the ChangeLog).

Price, M. N., Dehal, P. S., & Arkin, A. P. (2009). FastTree: Computing large minimum-evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution, 26(7), 1641–1650. https://doi.org/10.1093/molbev/msp077

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2: Approximately maximum-likelihood trees for large alignments. PLOS ONE, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490

Categories

biology, phylogenetics