|
Last change
on this file was
19532,
checked in by westram, 6 weeks ago
|
- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 tracker (only affects html version).
- found URLs.
- page titles
- warn about long titles.
- introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
- cleanup header sections in all helpfiles.
- fix and/or update several help files.
- document syntax of help sources.
- build issues:
- when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
- remove output files on error (including files below ARBHOME/lib).
- pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
- moves Tree admin + NDS menu entries to top of menu
- adds: log:branches/help@18783:19531
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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 http://www.microbesonline.org/fasttree/ |
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| 28 | |
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