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FastTree

swMATH ID: 28979
Software Authors: Price, M.N., Dehal, P.S., Arkin, A.P.
Description: FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. 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. FastTree is open-source software – you can download the code below. FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and Gascuel 2008) models of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the ”CAT” approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3’s ”SH-like local supports”).
Homepage: http://microbesonline.org/fasttree/
Related Software: ASTRAL-II; RAxML; BEAST; MLTreeMap; SEPP; Scoredist; pplacer; Quartets MaxCut; Seq-Gen; iGTP; PAUP*; BIONJ; BEAGLE; DEPP; PhyloGeoTool; INSTRAL; UShER; HmmUFOtu; TIPP; STEM-hy
Cited in: 10 Publications

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