[Blends-commit] r2845 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Jun 17 06:42:36 2011
New Revision: 2845

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2845
Log:
smile packaged as mlv-smile, raxml now official package

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=2845&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Jun 17 06:42:36 2011
@@ -493,18 +493,8 @@
 Published-DOI: 10.1093/bioinformatics/btp636
 
 Depends: raxml
-Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
-License: GPL
-X-Category: Phylogenetic analysis
-X-Importance: Inference of large trees
-Pkg-Description: Randomized Axelerated Maximum Likelihood
- RAxML is a program for sequential and parallel Maximum Likelihood-based
- inference of large phylogenetic trees. It has originally been derived
- from fastDNAml.
- .
- There are freely accessible web-servers available for RAxML at
- http://phylobench.vital-it.ch/raxml-bb/ and
- http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .
+
+Depends: mlv-smile
 
 Depends: axparafit
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
@@ -733,36 +723,6 @@
  .
  Java TreeView is an extensible viewer for microarray data in
  PCL or CDT format.
-
-Depends: smile
-Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
-Responsible: Steffen Moeller <moeller at debian.org>
-WNPP: 221492
-License: GPL
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/smile/trunk/
-Pkg-Description: infer motifs in a set of sequences
- SMILE is a tool that infers motifs in a set of sequences, according to some
- criteria. It was first made to infer exceptional sites as binding sites in
- DNA sequences. Since the 1.4 version, it allows to infer motifs written on
- any alphabet (even degenerate) in any kind of sequences.
- .
- The specificity of SMILE is to allow to deal with what we call structured
- motifs, which are motifs associated by some distance constraints.
- .
- Smile determines sequence motifs on the basis of a set of DNA, RNA or
- protein sequences. The work was originally described in the Journal of
- Computational Biology (2000) 7:345-362 and has since been developed
- further.
-  * No hard limit on the number of combinations of motifs to describe
-    subsets of sequences.
-  * The sequence alphabet may be specified.
-  * The use of wildcards is supported.
-  * Better determination of significance of motifs by simulation.
-  * Introduction of a set of sequences with negative controls
-    that should not match automatically determined motifs.
-Remark: We do not know anybody who actually uses SMILE and thus the
- packaging effort is stalled.  Feel free to tell us, if you are
- interested in turning this into an official package.
 
 Depends: cactus
 Homepage: http://www.cactuscode.org/Community/Biology.html