[Cdd-commits] r1088 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Sep 15 08:23:03 2008
New Revision: 1088

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


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Sep 15 08:23:03 2008
@@ -2703,3 +2703,39 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: prank
+Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
+License: GPL (except two algorithms)
+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: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
+ PRANK is a probabilistic multiple alignment program for DNA, codon
+ and amino-acid sequences. It's based on a novel algorithm that treats
+ insertions correctly and avoids over-estimation of the number of
+ deletion events. In addition, PRANK borrows ideas from maximum
+ likelihood methods used in phylogenetics and correctly takes into
+ account the evolutionary distances between sequences. Lastly, PRANK
+ allows for defining a potential structure for sequences to be aligned
+ and then, simultaneously with the alignment, predicts the locations
+ of structural units in the sequences.
+ .
+ PRANK is a command-line program for Unix-style environments but the
+ same sequence alignment engine is implemented in the graphical
+ program PRANKSTER. In addition to providing a user-friendly interface
+ to those not familiar with Unix systems, PRANKSTER is an alignment
+ browser for alignments saved in the HSAML format. The novel format
+ allows for storing all the information generated by the aligner and
+ the alignment browser is a convenient way to analyse and manipulate
+ the data.
+ .
+ PRANK aims at an evolutionarily correct sequence alignment and often
+ the result looks different from ones generated with other alignment
+ methods. There are, however, cases where the different look is caused
+ by violations of the method's assumptions. To understand why things
+ may go wrong and how to avoid that, read this explanation of
+ differences between PRANK and traditional progressive alignment
+ methods.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html