[Cdd-commits] r519 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Sun Jan 20 16:22:39 2008
New Revision: 519

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added four WNPPs as prospective packages


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Sun Jan 20 16:22:39 2008
@@ -187,4 +187,75 @@
  for common tasks in structural biology to facilitate the development of
  molecular modeling, design and analysis tools.
 	    
-     
\ No newline at end of file
+Depends: tacg
+Homepage: http://sourceforge.net/projects/tacg
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+License: GPL and others
+WNPP: 461504
+Pkg-Description: command line program for finding patterns in nucleic acids
+ tacg is a character-based, command line tool for unix-like operating systems
+ for pattern-matching in nucleic acids and performing some of the basic protein
+ manipulations. It was originally designed for restriction enzyme analysis of
+ DNA, but has been extended to other types of matching. It now handles
+ degenerate sequence input in a variety of matching approaches, as well as
+ patterns with errors, regular expressions and TRANSFAC-formatted matrices.
+ .
+ It was designed to be a grep for DNA and like the original grep, its
+ capabilities have grown so that now the author has to keep calling up the help
+ page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
+ application in any sense. However, it's existance as a strictly command-line
+ tool lends itself well to Webification and wrapping by various GUI tools and
+ it is now distributed with a web interface form and a Perl CGI handler.
+ Additionally, it can easily be integrated into editors that support shell
+ commands such as nedit.
+ .
+ The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
+ BMC Bioinformatics. 3:8  http://www.biomedcentral.com/1471-2105/3/8
+
+Depends: altree
+Homepage: http://claire.bardel.free.fr/software.html
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+License: GPL
+WNPP: 461506
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#altree
+Pkg-Description: program to perform phylogeny based analyses
+ This software was designed to perform phylogeny based analysis: first,
+ it allows the detection of an association between a candidate gene and
+ a disease, and second, it enables to make hypothesis about the
+ susceptibility loci.
+    
+Depends: treeplot
+Homepage: http://www.pge.cnrs-gif.fr/bioinfo/treeplot/
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+License: GPL
+WNPP: 461506
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot
+Pkg-Description: Phylogenetic tree file converter
+ Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
+ Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
+ (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
+ (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
+ file (.pnm)
+     
+Depends: treevolve
+Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
+Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
+License: has to be verified
+WNPP: 461510
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve
+Pkg-Description: simulation of evolution of DNA sequences
+ treevolve will simulate the evolution of DNA sequences under a
+ coalescent model, which allows exponential population growth,
+ population subdivision according to an island model, migration and
+ recombination. In addition different periods of population dynamics
+ can be enforced at different times. For example, a period of
+ exponential growth can be followed by a period of stasis where the
+ population is subdivided into demes. Multiple sets of such simulated
+ sequence data can then be compared to sequence data sampled from a
+ population of interest using suitable statistics, and various
+ evolutionary hypotheses concerning the evolution of this population
+ tested.
+ .
+ Citation: Population dynamics of HIV-1 inferred from gene sequences
+ Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
+