[Cdd-commits] r1064 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Sep  8 10:11:59 2008
New Revision: 1064

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


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  8 10:11:59 2008
@@ -2108,3 +2108,46 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Comment: BioLinux contains a clcworkbench package which is available
+ at http://www.clcbio.com/index.php?id=28 but this seems to be only
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: coalesce
+Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
+License: to be clarified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: outdated program to estimate population-genetic parameters
+ COALESCE fits the model which has a single population of constant
+ size, and estimates 4Nu, where N is the effective population size and
+ u is the neutral mutation rate per site. You may also want the
+ Postscript or the TeX file of the preprint version of the Kuhner,
+ Yamato, and Felsenstein 1995 paper.
+ .
+ The homepage contains the explicite link: "We are no longer
+ supporting COALESCE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however."  So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Depends: lamarc
+Homepage: http://evolution.gs.washington.edu/lamarc/
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimate population-genetic parameters
+ LAMARC is a program which estimates population-genetic parameters
+ such as population size, population growth rate, recombination rate,
+ and migration rates. It approximates a summation over all possible
+ genealogies that could explain the observed sample, which may be
+ sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
+ its sister program Migrate are successor programs to the older
+ programs Coalesce, Fluctuate, and Recombine, which are no longer
+ being supported. The programs are memory-intensive but can run
+ effectively on workstations.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html