output final adjusted phenotypes
multivar
output maps gender [averaged] [specific]
lm_map
output marker seeds only
genedrop
output overwrite pedigree file
output overwrite seed file
output pedigree chronological
pedcheck
output pedigree file
output pedigree record father mother
output pedigree record founder gene labels
output pedigree record mother father
output pedigree record trait latent variables
output pedigree record unobserved variables
output Rao-Blackwellized estimates file
output rescue data iterations
output rescue file
output score file
output scores every MC iterations
output scores file
output seed file
output spacing EM iterations
output statistics correlations
output statistics covariances
output trait seeds only
sample by scan
sample by step
select all markers
select all markers traits
select chromosome all markers
select chromosome all markers traits
select chromosome markers
select chromosome markers traits
select markers
select markers traits
select trait
select trait effects
select unlinked trait
set affected individuals
set affected individuals trait
set breeding convergence
set burn-in iterations
set chromosome locus window
ibddrop
set chromosome marker names
set chromosome markers frequencies
set component affected individuals
set component proband gametes
set component scoreset proband gametes
set component scoreset window patterns
set component window patterns
set eigenvalues
set genotyping error rate E
set ibd measures
lm_ibdtests
set ibd permutations
set ibd tests
set incomplete penetrances
markerdrop
set L-sampler probability
set locus window
set LRT stat iterations
set map estimation [with] [with no] mistyping
set marker data
set marker frequencies
set marker names
set marker seeds
set markers frequencies
set MC iterations
set normalized frequencies
set proband gametes
set pseudo-prior iterations
set pseudo-priors
set recombination frequencies
kin
set SA ascent iterations
set SA convergence
set SA curvature iterations
set SA gradient iterations
set sampler seeds
set scoreset proband gametes
set scoreset window patterns
set sequential imputation proposals every iterations
set test position window
set trait data discrete
set trait data genotypic
set trait data quantitative
set trait frequencies
set trait seeds
set traits additive variance
set traits frequencies
set traits genotype means
set traits residual variance
set window patterns
simulate chromosome markers traits
simulate markers
simulate markers trait
simulate markers traits
simulate markers using inheritance
simulate markers using trait
simulate unlinked trait
simulate unlinked traits
start additive correlations
start additive covariances
start additive variances
start residual correlations
start residual covariances
start residual variances
start trait effect
start trait mean