[Cdd-commits] r1106 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Sep 30 14:17:13 2008
New Revision: 1106

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added splitstree


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Sep 30 14:17:13 2008
@@ -595,9 +595,19 @@
 Depends: staden
 Homepage: http://staden.sourceforge.net/
 License: BSD
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
 Pkg-Description: DNA sequence assembly (Gap4), editing and analysis tools
  A fully developed set of DNA sequence assembly (Gap4), editing and
  analysis tools (Spin).
+ .
+ Staden is a suite of tools for sequence analysis. The main graphical
+ interfaces are called using the commands pregap4 and gap4. Staden
+ contains its own algorithms for activities such as base calling,
+ cleaning and assembling sequences, however other programs , such as
+ phred, phrap and cross_match can be run easily from within the
+ graphical interfaces. The default settings in this package assume
+ that phred and phrap are installed.
 
 Depends: dazzle
 Homepage: http://www.biojava.org/dazzle
@@ -2815,3 +2825,36 @@
  existence of this program and the even better alternative even if
  BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
  a package.
+
+Depends: splitstree
+Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Analyzing and Visualizing Evolutionary Data
+ Evolutionary data is most often presented as a phylogentic tree, the
+ underlying assumption being that evolution is a branching
+ process. However, real data is never ideal and thus doesn't always
+ support a unique tree, but often supports more than one possible
+ tree. Hence, it makes sense to consider tree reconstruction methods
+ that produce a tree, if the given data heavily favors one tree over
+ all others, but otherwise produces a more general graph that
+ indicates different possible phylogenies. One such method is the
+ Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
+ Dress (1992) and its variations. Another example is Spectral Analysis
+ developed by Hendy, Penny and others.
+ .
+ These and other methods are implemented in the program SplitsTree,
+ that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
+ Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
+ format.
+ .
+ Note: There is a new version 4.0 written from scratch at
+ http://www.splitstree.org/ which requires a license key - so this is
+ probably non-free.  Version 3.2 which is linked above has some
+ downloadable source code without any license or copyright statement -
+ so it has to be clarified whether we are able to distribute this code
+ or not.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html