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
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., and Arkin, A.P. (2009) FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077.
Freely available at MBE. Or see earlier version
Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.
Freely available at PLoS ONE. Or see earlier version.
- Validated 4/5/2018