[Blends-commit] r3362 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri May 25 12:15:47 2012
New Revision: 3362

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3362
Log:
Remove reduncant information from ecell and 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=3362&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri May 25 12:15:47 2012
@@ -348,6 +348,10 @@
 Depends: cluster3
 
 Depends: dazzle
+
+Depends: ecell
+
+Depends: fasttree
 
 Depends: forester
 
@@ -598,31 +602,6 @@
  .
  Ngila is published in Cartwright RA Bioinformatics 2007
  23(11):1427-1428; doi:10.1093/bioinformatics/btm095
-
-Depends: ecell
-Homepage: http://www.e-cell.org/
-Responsible: Steffen Moeller <moeller at debian.org>
-WNPP: 241195
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ecell/trunk/
-Pkg-Description: Concept and environment for constructing virtual cells on computers
- The E-Cell Project is an international research project aiming at
- developing necessary theoretical supports, technologies and software
- platforms to allow precise whole cell simulation.
- .
- The E-Cell System is an object-oriented software suite for modeling,
- simulation, and analysis of large scale complex systems such as
- biological cells, architected by Kouichi Takahashi and written by
- a team of developers.
- .
- The core part of the system, E-Cell Simulation Environment version 3,
- allows many components driven by multiple algorithms with different
- timescales to coexist.
- .
- E-Cell System consists of the following three major parts:
-  * E-Cell Simulation Environment (or E-Cell SE)
-  * E-Cell Modeling Environment (or E-Cell ME)
-  * E-Cell Analysis Toolkit.
 
 Depends: haploview
 Homepage: http://www.broad.mit.edu/mpg/haploview/
@@ -2771,29 +2750,6 @@
  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/
-Vcs-Svn: svn://svn.debian.org/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").
-
 Depends: microbiomeutil
 Homepage: http://microbiomeutil.sourceforge.net/
 License: free