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To: Multiple recipients of list HUM-MOLGEN <HUM-MOLGEN@NIC.SURFNET.NL>
Subject: COMP: Genetic analysis programs
From: Jurg Ott <ott@linkage.cpmc.columbia.edu>
Date: Fri, 23 Feb 1996 08:19:37 -0500

Date: Thu, 22 Feb 1996 14:52:19 +0000 (GMT)
From: Joseph D. Terwilliger <joe@well.ox.ac.uk>

Subject:

UPDATE ANNOUNCEMENT FOR LINKAGE DISEQUILIBRIUM ANALYSIS PROGRAMS
AND ANALYZE PROGRAMS

A new version of the programs DISLAMB and DISMULT for likelihood
based linkage disequilibrium analysis is now available via ftp.

Additionally a VMS version of ANALYZE has been released today
as well, for those who use VMS systems - available from the same ftp
sites.

NEW PROGRAM VERSION  2-22-96
Updates include

        1) Improved maximization routine included after bug
           report from Michael Knapp

        2) Floating Point arithmetics streamlined following
           programming suggestions from Alejandro Schaffer

        3) Haplotype Relative Risk analysis programs included
           for disequilibrium analysis using LINKAGE pedigree
           files.

        4) Support Intervals for Lambda and Theta are now
           computed by DISLAMB.

        5) Cross system compatibility improved.

        6) Executables now available with statically linked
           libraries for SUNOS, SOLARIS, and OSF, so no PASCAL
           compiler is required - VMS version, however does
           require a PASCAL compiler installed on your machine.

If there are questions, refer them to

Joseph D. Terwilliger
Wellcome Trust Center for Human Genetics
Windmill Road
Headington OX3 7BN
Oxford, UK

FAX +44 - 1865 - 742 196
Ph. +44 - 1865 - 740 016
EMAIL joe.terwilliger@well.ox.ac.uk

OR

Joseph D. Terwilliger
Columbia University, Unit 58
722 West 168th Street
New York, NY  10032
USA

FAX +1 - 212 - 568-2750
Ph. +1 - 212 - 960-5863
EMAIL jdt3@columbia.edu

To get the programs and documentation for DEC and SUN machines under
either UNIX or VMS, just do the following:

>From OXFORD:

1)   ftp ftp.well.ox.ac.uk
2)   login as anonymous with your EMAIL address as the password

        (please leave your EMAIL address so I have a record of who
         has downloaded the programs)

3)   cd pub/genetics/diseq
4)   binary
5)   get FILENAME.tar.Z
6)   close
7)   quit

>From NEW YORK

1)   ftp linkage.cpmc.columbia.edu
2)   login as anonymous with your EMAIL address as the password

        (please leave your EMAIL address so I have a record of who
         has downloaded the programs)

3)   cd software/diseq
4)   binary
5)   get FILENAME.tar.Z
6)   close
7)   quit

Then, on your own machine

uncompress FILENAME.tar.Z
tar xvf FILENAME.tar

There are a number of files available, as follows:

SYSTEM_diseq.tar.Z = source, executables, and documentation
SYSTEM_diseq_source.tar.Z = source and documentation

Files are available for the following SYSTEMs - OSF,SOLARIS,
SUNOS, VMS.  The SUNOS_diseq_source.tar.Z contains a fairly
standard UNIX version of the code which could be recompiled
with minimal or no changes (involving file handling if anything
for some systems...) on your different UNIX system.  If you download
only the source files, then they will be in a directory
SYSTEM_diseq/source.  You shouls first create a directory
SYSTEM_diseq/exec, and then to compile the programs, go to the
SYSTEM_diseq/source directory and run the included shell script
"compilethem" which will compile the programs and put the executables
in the directory SYSTEM_diseq/exec which you just created.

There are seven programs included

1) DISLAMB for single locus linkage disequilibrium analysis for a multiallelic s
ystem

2) DISMULT for multilocus linkage disequilibrium analysis

3) TDTLIKE for multiallelic likelihood-based version of the TDT test for linkage
   in pedigree material.

4) MCNMULT for multilocus-multiallelic likelihood-based version of the
   McNemar test for linkage disequilibrium in pedigree material.

5) HRRPREP - takes LINKAGE format pedigree file pedin.dat and LINKAGE format
   parameter file datain.dat, and from each pedigree selects one proband
   by looking for the first affected person in the pedigree typed at the first
   marker locus with parents also typed at that locus, and take his alleles as
   the case sample, and the nontransmitted alleles from the parents as the
   control sample (cf. Falk and Rubinstein, 1987; Terwilliger and Ott, 1992).

6) HRRLAMB - same as DISLAMB but taking the data from diseqin.dat created by
   HRRPREP - note - this program only analyzes the first marker locus in your
   pedin.dat file.

7) HRRMULT - same as DISMULT but takes the data from the diseqin.dat created by
   HRRPREP (note that the recombination fractions between markers are assumed
   to have been given in the parameter file, datain.dat.

DISLAMB and DISMULT are discribed in the documentation file diseq.doc, and TDTLI
KE
and MCNMULT are described in the file tdtlike.doc   All these programs are
based on algorithms largely presented in the following papers which should
be cited when using them:  HRRMULT and HRRLAMB are the same algorithm as DISLAMB
and DISMULT, but the sampling of cases and control is done by HRRPREP according
to
the method outlined in Terwilliger and Ott, 1992.

FOR ALL OF THESE PROGRAMS CITE:

Terwilliger, JD  (1995) " A Powerful Likelihood Method for the Analysis of Linka
ge
Disequilibrium Between Trait Loci and One or More Polymorphic Marker Loci" Am J
Hum
Genet 56:777-787.

Terwilliger, JD (1996) "Response to Sham et al." Am J Hum Genet (In Press - May
1996).

FOR TDTLIKE or MCNMULT, quote the above articles plus

Terwilliger, JD (1996) " Pedigree-based Likelihood Methods for Analysis
of Linkage and Linkage Disequilibrium with One or More Marker Loci"
(Submitted)

FOR HRRPREP, HRRMULT, and HRRLAMB quote the first two articles plus

Falk CT, and Rubinstein P (1987) "Haplotype relative risks: an easy reliable way
 to
construct a proper control sample for risk calculations" Ann Human Genet 51:227-
233.

Terwilliger JD and Ott J (1992) "A haplotype-based haplotype relative risk stati
stic"
Human Heredity 42:337-346.


   
 
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