[Blends-commit] r2696 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Thu Mar  3 13:20:23 2011
New Revision: 2696

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2696
Log:
Added fasttree

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2696&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Thu Mar  3 13:20:23 2011
@@ -3619,6 +3619,28 @@
  accurately provides taxonomic assignments from domain to genus, with
  confidence estimates for each assignment.
 
+Depends: fasttree
+Homepage: http://www.microbesonline.org/fasttree/
+License: GPL-2+
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/fasttree/trunk/
+Pkg-Description: phylogenetic trees from alignments of nucleotide or protein sequences
+ FastTree infers approximately-maximum-likelihood phylogenetic trees from
+ alignments of nucleotide or protein sequences. It handles 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 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) model 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").
 
 
 Comment: Several related R packages are listed at CRAN: