As of 02.14.03 we do not have a Pascal compiler for Linux, therefore there is no
functional Linkage software for our Linux OS machines. One can install it in own
working PC, by having in advance the PC compiler. (A.K.)
This is an interesting note from
http://bimas.dcrt.nih.gov/linkage/ltools.html#linkage
LINKAGE Version 5.1, dated January 19, 1994:
NOTE: It is strongly recommended that the use of the LINKAGE program be
discontinued and FASTLINK (and/or VITESSE) be used in it's place. The
functionality of FASTLINK is designed to supercede LINKAGE, and FASTLINK's
performance benefits are very great. And for those problems which VITESSE can
accomodate, the additional performance has the potential for being still greater.
LINKAGE is an integrated system of programs designed to perform linkage
analysis and genetic risk calculation for an arbitrary number of loci. These
programs are subdivided as "Linkage Analysis" programs and "Linkage Support"
programs.
LINKAGE's Linkage Analysis programs
Linkage Analysis programs consist of a core of programs, which perform such
tasks as maximum likelihood estimation of recombination rates, calculation of lod
score tables, and analysis of genetic risk.
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MLINK: This program performs n-point linkage and risk calculations in
general pedigrees. This program can be used to construct lod score tables.
LODSCORE: This program performs iterative maximum likelihood
estimation of recombination fractions from two-locus data in general
pedigrees.
ILINK: This program performs iterative maximum likelihood estimations
in general pedigrees.
LINKMAP: This program calculates location scores in general pedigrees.
UNKNOWN: This program infers possible genotypes for unknown
individuals. Prepares input files for ILINK, LINKMAP, MLINK and
LODSCORE programs.
CILINK: This program performs iterative maximum likelihood
estimations in nuclear pedigrees (nuclear families with the possible
addition of grandparents).
CMAP: This program calculates likelihoods for genetic location in nuclear
pedigrees.
CINFER: This program infers genotypes for unknown individuals
whenever possible. Works on nuclear pedigrees only. Prepares the input
file for the CFACTOR program.
CFACTOR: This program applies factorization and transformation rules to
genotypes in nuclear pedigrees prior to analysis with the CMAP and
CILINK programs. CFACTOR works on nuclear pedigrees only.
LINKAGE's Linkage Support Programs
Linkage Support programs form an interactive "shell" or "front-end" around the
core programs. In addition, they also provide the user with linkage file
preparation, data checking facilities and report generation from the linkage
results.
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LCP: Linkage Control Program (LCP) is an interactive menu program for
building command files to perform linkage analysis.
LRP: Linkage Report Program (LRP) is an interactive menu program for
displaying and formatting the stream output from the linkage analysis
programs.
MAKEPED: converts pedigree files of the form: pedigree number, ID
number, father ID, mother ID to a form that includes offspring and sibpointers.
PREPLINK: interactively defines locus descriptions; stores descriptions in
a parameter file for input into computational programs.
LINKAGE references:
G. M. Lathrop, J.-M. Lalouel, C. Julier, and J. Ott, Strategies for Multilocus
Analysis in Humans, PNAS 81(1984), pp. 3443-3446.
G. M. Lathrop and J.-M. Lalouel, Easy Calculations of LOD Scores and Genetic
Risks on Small Computers, American Journal of Human Genetics, 36(1984), pp.
460-465.
G. M. Lathrop, J.-M. Lalouel, and R. L. White, Construction of Human Genetic
Linkage Maps: Likelihood Calculations for Multilocus Analysis, Genetic
Epidemiology 3(1986), pp. 39-52.
For more information, look at genetic linkage analysis software at Rockefeller
University.