Installation instructions:

multisim.f is a Fortran program which uses the NAG Fortran library.
To install the program, you must first compile it and link it with the 
NAG library, e.g.,

f77 -O -o multisim multisim.f -lnag

Running multisim:

The program 'multisim' is completely prompt-driven, with only a single
exception.  The file seed.dat must be present in the directory in
which you run 'multisim'.  This file contains an integer seed for the
random number generator.  If you use the same seed for every run, you
will get identical datasets for every run.  This allows you to
reproduce any given simulation, provided you know which seed you've
used.

The various genotype files take the following form, and are compatible
with Mapmaker/SIBS format:

1st field: family #
2nd field: individual ID # within family
3rd field: father's ID #
4th field: mother's ID #
5th field: sex (1=MALE, 2=FEMALE); offspring are always coded 2, since
           sex-limitation models are not yet an option
6th field: affection status, always 0 (for compatibility with SIBS format)
7-8:       allele 1 and allele 2 for locus 1
9-10, etc: allele 1 and allele 2 for locus 2-last

The simulator outputs various different genotype files, as described:

pedigree.dat:      standard file with only marker genotypes
pedigree-[2-6].dat: pedigree.dat file for chromosomes 2-6
genotypes.dat:     same as pedigree.dat, but includes the QTL genotypes in
                   the appropriate positions
qtl-genotypes.dat: file with only the QTL genotypes
complete-info.dat: complete information genotypes of markers and QTLs
                   This means that mother is always genotype 1,2 and
                   father is always genotype 3,4, at markers and QTLs
complete-marker-info.dat: same as complete-info.dat, but excluding QTLs
no-parents.dat:    same as pedigree.dat, but with parental genotypes
                   scored 0,0, or missing
no-parents-[2-6].dat: no-parents.dat file for chromosomes 2-6
one-parent.dat:    same as pedigree.dat, but with father's genotype
                   scored 0,0, or missing
one-parent-[2-6].dat:  one-parent.dat file for chromosomes 2-6
internal.loc:      Mapmaker/SIBS-style locus description file for
                   chromosome 1
internal-[2-6].loc: same as internal.loc, for chromosomes 2-6

The file pheno.dat is always generated, which is of the same form as
expected by Mapmaker/SIBS.  That is, the first line contains the
number of phenotypes (n) in the file, and each following line takes
the form:

1st field:     family #
2nd field:     sib #
3rd-nth field: phenotypic value for phenotypes 1 through n-2


Some notes on the simulation procedure:

The program requires effect sizes for each QTL to be specified, in the
form of a separate score for each of the AA, Aa, and aa genotypes.  It
also requires input of a total heritability across all QTLs, a
polygenic heritability (of QTLs not specified), and proportion of
shared environmental variance.  The simulator then scales polygenic
and environmental variances to accommodate the specification.  There
is also facility for simulating the interaction between two loci.
Having selected the epistatis option, by setting the genotypic values
of the first locus involved in the interaction to all zeros, you would
enter scores for each of the 9 possible genotypic combinations.


Batch processing:

The program reads from standard input.  An alternative to using
multisim interactively is to prepare a batch file, e.g., 3pheno.input
(supplied) and redirect it into multisim, i.e.

multisim < 3pheno.input
