> I have gotten quite a few responses to my question about running a linkage
> analysis with a large number of alleles (more than 14). The most
> useful of these was to switch to using the FASTLINK package. The only
> drawback to doing this is that the FASTLINK package was written for use on
> a UNIX machine, and all that we have available to us is a VMS machine.
The other drawback is that you simply can't go on increasing your number
of alleles indefinitely, even on a large machine. FASTLINK does take a lot of
memory - it can use swap space, but then you need a lot of free disk space and
that is much slower than free memory, and although FASTLINK is much faster than
LINKAGE, any of these computations slow down with increasing numbers of
> Reworking these programs for a VMS machine is not a particularly difficult
> task, but it is time consuming. Therefore, is there anyone who has already
> done this who could warn me of some roadblocks which might make this
> process easier?
Yes, we have FASTLINK up & running under VMS. We only have gone through
the exercize for version 1.0, but I think the VMS-specific changes are included
in the FASTLINK documentation. We sent them on to Alex Schaffer since we
were (I think) the first to do a VMS implementation.
Div of Medical Genetics, RG-25
and Dept of Biostatistics
University of Washington
Seattle, WA 98195
wijsman at u.washington.edu