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Last change
on this file was
18839,
checked in by westram, 3 years ago
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- upgrade FastTree to version 2.1.11
- cleanup: define flags and use make variables.
- specify fasttree version in help.
- update changelog.
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File size:
1.2 KB
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| 1 | Fasttree |
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| 2 | |
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| 3 | DESCRIPTION |
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| 4 | |
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| 5 | FastTree infers approximately-maximum-likelihood phylogenetic trees from |
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| 6 | alignments of nucleotide or protein sequences. FastTree can handle alignments |
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| 7 | with up to a million of sequences in a reasonable amount of time and memory. |
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| 8 | For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. |
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| 9 | |
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| 10 | FastTree is more accurate than PhyML 3 with default settings, and much more accurate |
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| 11 | than the distance-matrix methods that are traditionally used for large alignments. |
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| 12 | FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of |
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| 13 | nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), |
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| 14 | or LG (Le and Gascuel 2008) models of amino acid evolution. |
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| 15 | To account for the varying rates of evolution across sites, |
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| 16 | FastTree uses a single rate for each site (the "CAT" approximation). |
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| 17 | To quickly estimate the reliability of each split in the tree, FastTree computes |
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| 18 | local support values with the Shimodaira-Hasegawa test (these are the |
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| 19 | same as PhyML 3's "SH-like local supports"). |
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| 20 | |
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| 21 | VERSION |
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| 22 | |
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| 23 | Currently Version 2.1.11 is delivered with arb. |
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| 24 | |
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| 25 | DETAILS |
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| 26 | |
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| 27 | For details please refer to LINK{http://www.microbesonline.org/fasttree/} |
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| 28 | |
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