HUM-MOLGEN archive: COMP: Genetic analysis programs

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.