[Blends-commit] r2667 - in /projects/med/trunk/debian-med/tasks: bio bio-dev

[tille at users.alioth.debian.org]

Author: tille
Date: Sat Feb 12 18:21:17 2011
New Revision: 2667

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2667
Log:
Added ClonalFrame and JEBL

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2667&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Feb 12 18:21:17 2011
@@ -3469,6 +3469,25 @@
  ancestry.
 Published-URL: http://www.genetics.org/cgi/content/abstract/genetics.110.120121v1
 
+Depends: clonalframe:
+License: GPLv3
+Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clonalframe/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clonalframe/trunk/?rev=0&sc=0
+Pkg-Description: inference of bacterial microevolution using multilocus sequence data
+ ClonalFrame identifies the clonal relationships between the members of
+ a sample, while also estimating the chromosomal position of homologous
+ recombination events that have disrupted the clonal inheritance.
+ .
+ ClonalFrame can be applied to any kind of sequence data, from a single
+ fragment of DNA to whole genomes. It is well suited for the analysis of
+ MLST data, where 7 gene fragments have been sequenced, but becomes
+ progressively more powerful as the sequenced regions increase in length
+ and number up to whole genomes. However, it requires the sequences to be
+ aligned. If you have genomic data that is not aligned, we recommend
+ using Mauve which produces alignment of whole bacterial genomes in
+ exactly the format required for analysis with ClonalFrame.
+
 Depends: abacas
 Homepage: http://abacas.sourceforge.net/
 License: GPL

Modified: projects/med/trunk/debian-med/tasks/bio-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-dev?rev=2667&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev (original)
+++ projects/med/trunk/debian-med/tasks/bio-dev Sat Feb 12 18:21:17 2011
@@ -199,3 +199,18 @@
  The LibSBML code is very portable and is supported on Linux, Windows
  (native), and Mac OS X.
 
+Depends: libjebl2-java
+License: LGPL
+Homepage: 
+WNPP: 613080
+Homepage: http://code.google.com/p/jebl2/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libjebl2-java/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libjebl2-java/trunk/
+Pkg-Description: Java Evolutionary Biology Library
+ A Java library for evolutionary biology and bioinformatics, including
+ objects representing biomolecular sequences, multiple sequence
+ alignments and phylogenetic trees.
+ .
+ This is a branch of the original JEBL on
+ http://sourceforge.net/projects/jebl/ to develop a new API and class
+ library.