[Blends-commit] r3368 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Sun May 27 08:00:24 2012
New Revision: 3368

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3368
Log:
Remove now reduncant information

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=3368&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun May 27 08:00:24 2012
@@ -381,6 +381,14 @@
 
 Depends: patristic
 Language: Java
+
+Depends: pcma
+Enhances: t-coffee
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+ .
+ Check with authors about licensing, they adopted code from clustalw which is now
+ free.  Thus a change might be possible
 
 Depends: proalign
 
@@ -2495,30 +2503,6 @@
  Tool options may change in the next release. Version 1 tool options
  will remain supported wherever possible in order to preserve
  operation of any existing scripts.
-
-
-Depends: pcma
-Homepage: ftp://iole.swmed.edu/pub/PCMA/
-License: non-free for commercial
-Enhances: t-coffee
-Pkg-Description: fast and accurate multiple sequence alignment based on profile consistency
- PCMA (profile consistency multiple sequence alignment) is a progressive
- multiple sequence alignment program that combines two different
- alignment strategies. Highly similar sequences are aligned in a fast way
- as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
- applied to align the relatively divergent groups based on
- profile–profile comparison and consistency. The scoring function for
- local alignments of pre-aligned groups is based on a novel
- profile–profile comparison method that is a generalization of the
- PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
- and accuracy in a flexible way and is suitable for aligning large
- numbers of sequences.
-Published-URL: http://bioinformatics.oxfordjournals.org/content/19/3/427.short
-Remark: Precondition for T-Coffee
- see http://wiki.debian.org/DebianMed/TCoffee
- .
- Check with authors about licensing, they adopted code from clustalw which is now
- free.  Thus a change might be possible
 
 Depends: fas
 Homepage: http://fsa.sourceforge.net/