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17 lines
1 KiB
Text
17 lines
1 KiB
Text
FastTree infers approximately-maximum-likelihood phylogenetic trees from
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alignments of nucleotide or protein sequences. FastTree can handle
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alignments with up to a million of sequences in a reasonable amount of
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time and memory. For large alignments, FastTree is 100-1,000 times
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faster than PhyML 3.0 or RAxML 7. FastTree is open-source software.
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FastTree is more accurate than PhyML 3 with default settings, and much
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more accurate than the distance-matrix methods that are traditionally
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used for large alignments. FastTree uses the Jukes-Cantor or generalized
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time-reversible (GTR) models of nucleotide evolution and the JTT
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(Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and
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Gascuel 2008) models of amino acid evolution. To account for the varying
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rates of evolution across sites, FastTree uses a single rate for each
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site (the "CAT" approximation). To quickly estimate the reliability of
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each split in the tree, FastTree computes local support values with the
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Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local
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supports").
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