Linkage Newsletter 9(1), Feb 1995
wl101 at namaste.cc.columbia.edu
Tue Feb 7 11:33:13 EST 1995
| Linkage Newsletter |
Vol. 9 No. 1 February 1995
Published by Jurg Ott, Columbia University, New York
Editorial Assistant: Katherine Montague
E-mail: jurg.ott at columbia.edu
Columbia University, Unit 58
722 West 168th Street, New York, NY 10032
In 1995, the following linkage courses will be held:
February 27 - March 3: Introductory course at the Universi-
ty of Zurich (Switzerland), Irchel Campus Computer Center. This
course is full.
June 12-16: Introductory course at Columbia University, New
York (maximum of 30 participants). We often receive many more
applications than we can accept and will carry this course twice
in case of high demand (date not yet set).
October 2-6: Advanced course at the University of Zurich
(Switzerland), Irchel Campus Computer Center.
The next Advanced course at Columbia University will be held
early in January 1996.
To obtain information on these courses, please write to
Katherine Montague, course coordinator, by e-mail or fax. The
textbook to be used for theoretical background and course exer-
cises is Terwilliger JD & Ott J: Handbook of Human Genetic
Linkage, Johns Hopkins University Press, 1994 (additional materi-
al for advanced courses will be handed out at the course).
Course participants are expected to bring this book with them to
the course; in case of problems please contact Katherine Monta-
UPGRADING OUR ftp SITE
Our anonymous ftp site (york.cpmc.columbia.edu) runs on an old
Vaxstation 3100 with ftp software that is not well adapted to the
system. Unfortunately, the Vaxstation occasionally freezes up
and must be rebooted -- there is evidently little that can be
done about this. So, if you experience problems accessing the
ftp site, please try again later. Also, accessing it at night or
in the morning tends to be more successful than at peak hours.
A new member of our team, Dr. Wentian Li, started installing
a new anonymous ftp site on our Sparcstation IPC. It is expected
to be much more stable then the current one. Furthermore, it
runs under Unix rather than under VMS as on the Vaxstation. As
soon as a larger hard disk is installed, we will transfer all
files from the Vaxstation to the Sparcstation. When ready, the
anonymous ftp site can be reached as linkage.cpmc.columbia.edu
and the old site (york.cpmc.columbia.edu) will be taken out of
service. The new ftp site is expected to be up by mid-March.
We regularly receive requests for the ESPA program, which carries
out affected sib pair analysis with estimation of unobserved
parental marker genotypes. This pro-gram is not available from
us -- please address any requests to the developer of ESPA, Dr.
Lodewijk Sandkuyil (sandkuyl at rullf2.LeidenUniv.nl), Voorstraat 27
a, 2611 JK Delft, The Netherlands. Tel: 011,31-15-123 638,
Bug in LINKAGE regarding loops
Dr. Alejandro Schaffer submitted the following report:
The purpose of this message is to report a dangerous bug in LINKAGE.
The bug is that if maxloop is set to a number strictly lower than the
actual number of loops, then LINKAGE gives no warning. In some cases it
will give plausible but incorrect results. In contrast, in FASTLINK if
maxloop is set to a number strictly lower than the actual number of
loops, the program gives a warning and exits with instructions on how to
fix the problem, without computing anything.
Editor's note: Readers of the Newsletter (January 1992) have
been made aware of this problem. However, thus far no test had
been implemented in LINKAGE to catch the situation that maxloop
is smaller than the actual number of loops. This test has now
been implemented in the DOS version of LINKAGE (available on our
ftp site) and will be implemented shortly in other LINKAGE
Newer versions of FASTLINK
The following announcement was submitted by Dr. Alejandro Schaf-
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
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
Like FASTLINK 2.1, this version is being distributed from a computer at
Rice University. Here are the instructions for retrieving the code:
Login as anonymous and leave your full e-mail address as password.
In that directory you will find various files. You can get everything
at once by retrieving the file:
and then (outside of ftp) doing the commands:
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. 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
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, Jurg Ott, Steve Roberts, Joe Terwilliger, Gerard
Tromp, Ellen Wijsman, Xiaoli 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!
We are also distributing executable versions of FASTLINK for DOS. The
ftp instructions are similar. Instead of doing
In that directory you will find 13 files. One is an executable for
UNKNOWN (called unknown.exe). We have 3 versions each of LODSCORE,
ILINK, LINKMAP, and MLINK with the constant maxhap set to 48, 96, 250
respectively. For example, the file li96.exe is LINKMAP with maxhap set
to 96 and the file il250.exe is ILINK with maxhap set to 250. maxhap is
the maximum product allowed for the number of alleles at each locus.
For example, if you want to a 3-locus analysis with 2x4x8=64 alleles,
you should not use the versions with maxhap set to 48, but you can use
either the 96 or 250 versions.
Alejandro Schaffer, PhD
Department of Computer Science
Houston, TX 77251
schaffer at cs.rice.edu
Phone: (713) 527-8101 x3813
FAX: (713) 285-5930
Compiling with the 'colig.bat' batch program
Dr. Joseph Terwilliger made me aware of a problem with the
'colig' batch program that we distribute to facilitate recompil-
ing the LINKAGE programs for DOS (Turbo/Borland Pascal):
I have a question for you about the turbo pascal colig.bat file. Why
does it have the line del *.tp* at the end? This seems to delete
turbo.tpl, which is needed to compile the programs here on the PC's in
Finland. Is it okay to change that line to DEL *.TPU instead of TP*, to
preserve the *.TPL files?
Response: When the LINKAGE programs are compiled with Tur-
bo/Borland Pascal, intermediate files are created and are left on
the hard disk. These files are named *.tpx, where x=U for
regular Turbo Pascal, x=P when compiled for protected mode, and
x=W when compiled to run under Windows. The statement 'del
*.tp*' deletes any of these files that might have been created.
This procedure was chosen under the assumption that the compiler
would reside in a different directory. If it resides in the same
directory as the programs to be compiled, one of the compiler
files, 'turbo.tpl', will also be deleted. Thus, the 'colig.bat'
and 'colit.bat' batch programs have now been restructured so that
'turbo.tpl' will no longer be deleted.
The following announcement has been submitted to the Newletter by
the meeting organizers:
Fourth Annual meeting of the INTERNATIONAL GENETIC EPIDEMIOLOGY SOCIETY,
June 20-22, 1995 - Snowbird, Utah. The meeting will be held in the
Cliff Lodge (just 29 miles from Salt Lake City International Airport) in
conjunction with the Society of Epidemiological Research. Abstracts for
consideration of oral presentations and posters are due February 10,
1995. For abstract forms, contact Michele Brown, University of Utah,
(801) 581-558099 or fax (801) 581-3165. For program information contact
Melissa Austin, University of Washington, Seattle, (206) 685-9384, fax
Support through grant HG00008 from the National Center
for Human Genome Research is gratefully acknowledged.
Wentian Li, Ph.D tel: 212-960-2200 ext 490
Associate Research Scientist 212-960-2507 (main office)
Department of Psychiatry FAX: 212-568-2750
More information about the Gen-link