Free software for linkage analysis in large pedigrees
Claus S. Jensen
claus at cs.auc.dk
Tue Nov 19 18:47:14 EST 1996
BLOCK v. 1.0.0
LINKAGE ANALYSIS IN LARGE COMPLEX PEDIGREES
Version 1.0.0 of 'block' (linkage analysis in large complex pedigrees)
is now available.
New in this version (IMPORTANT)
IMPORTANT : serious bugs are fixed with this version. If you use the
programs of this package, you must upgrade.
Much has been fixed or changed with this version (first beta) :
- some internal limits on string lengths have been raised, leading
to fewer crashes.
- an important error causing 'block' to exit wrongly was removed.
- some serious memory allocation bugs were removed.
- a small bug was fixed in 'theta' leading to variance estimates slightly
- better method for finding the starting configuration has been
implemented. This method almost always works in polynomial time,
and will soon be documented in a paper.
- additions to documentation. New informative examples are given.
- pedigree example 'ped_ex4' has been extended to specify necessary
blocks for irreducibility.
- it is now possible to specify options within the pedigree specification
file, prepending them with '%'. The format is described in the manual,
Section 2. An example of this can be seen in 'ped_ex5'.
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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