Since May 1993, we have been distributing faster versions of the
genetic linkage analysis programs in LINKAGE 5.1. Several users have
dubbed the new code "FASTLINK".
Version 2.2 of FASTLINK is now ready and available. The changes
from version 2.1 (distributed in March 1994) include:
1. Bug fixes to bugs introduced in FASTLINK and bugs inherited from LINKAGE
2. More dynamic memory allocation
3. More diagnostics to detect user errors politely
4. Crash-recovery is now possible for LINKMAP and MLINK, in addition
to LODSCORE and ILINK
5. Lots of information about portability of FASTLINK to different
operating systems is included
6. A document entitled "The Mystery of (the) Unknown" explaining how the
preprocessor program UNKNOWN works
among other goodies.
See the file README.updates, which comes with the distribution, for details.
Like FASTLINK 2.1, this version is being
distributed from a computer at Rice University.
Here are the instructions for retrieving the code:
ftp softlib.cs.rice.edu
Login as anonymous and leave your full e-mail address as password.
cd pub/fastlink
In that directory you will find various files.
You can get everything at once by retrieving the
file:
fastlink.tar.Z
and then (outside of ftp) doing the commands:
uncompress fastlink.tar.Z
tar xvf fastlink.tar
If you prefer to get your files piecemeal, instead of getting
fastlink.tar.Z start by getting README* The file README (with no
extension) will give you a roadmap to all the documentation
Most of the changes from version 1.1 to 2.0 are described in the paper:
A. A. Schaffer, S. K. Gupta, K. Shriram, and R. W. Cottingham Jr.
Avoiding Recomputation in Linkage Analysis, Human Heredity, 44(1994),
pp. 225-237.
Our initial improvements are described in the paper:
R. W. Cottingham Jr., R. M. Idury, A. A. Schaffer. Faster Sequential
Genetic Linkage Computations, American Journal of Human Genetics 53(1993),
pp. 252-263.
We ask you to cite both papers if you use FASTLINK in any
published experiments. Both papers are included in the distribution.
The code in this distribution is the result of complicated
collaborative work in which all 5 authors of the above papers played
significant roles.
FASTLINK is a modified version of LINKAGE. You should continue to
cite the original papers on LINKAGE, if you used FASTLINK in a published
experiment.
I am maintaining a mailing list of FASTLINK users. If you have retrieved the
code and would like to be on the mailing list, send me e-mail at the address
below.
Special thanks to many FASTLINK users including: Lucien Bachner, Alan
Cox, David Featherstone, Sandep Gupta, Victoria Haghighi, Carol
Haynes, Jerry Halpern, Kimmo Kallio, Luc Krols, Shriram Krishnamurthi,
Tara Cox Matise, Ken Morgan, Jeremy Murray, Jurg Ott, Steve Roberts,
Joe Terwilliger, Gerard Tromp, Ellen Wijsman, Xiali Xie, who provided
bug reports, suggestions for improvements, guidance on documentation,
and assistance with portability. I could not have prepared FASTLINK
2.2 without your help!
Alejandro Schaffer, PhD
Department of Computer Science
Rice University
Houston, TX 77251
schaffer at cs.rice.edu
