Free software for linkage analysis in general pedigrees
Claus S. Jensen
claus at cs.auc.dk
Fri Jan 17 02:57:33 EST 1997
BLOCK v. 1.0.1
PEDIGREE (LINKAGE) ANALYSIS IN LARGE COMPLEX PEDIGREES
Version 1.0.1 of 'block' (pedigree (incl. linkage) analysis in large complex
pedigrees) is now available.
Pedigree files can now be specified as, e.g., 'peds/ped_ex1', instead of
only 'ped_ex1', i.e., by using the absolute path.
A new technical report has been written, documenting the use of 'block'
in linkage analysis:
Claus S. Jensen and Augustine Kong : "Blocking Gibbs Sampling for
Linkage Analysis in Large Pedigrees with Many Loops", Technical Report
R96-2048. Department of Computer Science, Aalborg University, Denmark.
It can be obtained from http://www.cs.auc.dk/~claus/articles.html or
by anonymous ftp from ftp.cs.auc.dk/pub/reports/tech-reports/
Several memory allocation bugs have been fixed, some important.
The program 'block' implements an algorithm called blocking Gibbs
sampling. The method is based on the Markov chain Monte Carlo method,
Gibbs sampling, but combines this stochastic method with exact local
computations (e.g., peeling) to get a method that can successfully
handle very large and complex (e.g., inbred) pedigrees (thousands of
individuals). The method allows the user to test the presence of
linkage between two genes.
As this is a relatively new and untested program, there are bound to be
errors and other problems. All these should of course be reported to me.
For more information, contact me, or download the program
The program is available for the architectures : Linux ELF,
Sparc Solaris, IRIX 64, MS-DOS, and IBM RS/6000 AIX 3.2.5.
There is also a homepage associated with the program at
Claus Skaanning Jensen
Claus Skaanning Jensen, Ph.D.-student at Aalborg University, Denmark
claus at iesd.auc.dk, http://www.iesd.auc.dk/~claus
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