sample by scan
sample by step
select [chromosome] all markers
select [chromosome] markers
select inheritence
markerdrop
select trait
multivar
set batches MC variance estimation
set [chromosome] locus window
ibddrop
set [chromosome] marker allele frequencies
genedrop
set [chromosome] marker names
set [component] [scoreset] window patterns
set [component] proband gametes
set [component] scoreset proband gametes
set breeding convergence
set burn-in iterations
set debug level
set debug libname
set debug main
set eigenvalues
set EM convergence
lm_map
set genotyping error rate
set global MCMC
set ibd measures
lm_ibdtests
civil
set ibd permutations
set ibd tests
set inheritance tlocs
set L-sampler probability
set likelihood-ratio lambda-p model gridpoints
set likelihood-ratio measures
set likelihood-ratio tests
set limit for exact computation
set LRT statistics iterations
set map estimation with [no] mistyping
set marker data
set marker seeds
set MC iterations
set MCMC markers only
set normalized allele frequencies
set permutation seeds
set printlevel
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 sequential imputation proposals every iterations
set test position window
set tlocs allele frequencies
set trait data
set trait data discrete
set trait effects
set trait for tlocs joint genotype means
set trait seeds
set traits additive variance
set traits for tlocs genotype means
set traits for tlocs incomplete penetrances
set traits multiple tlocs
set traits residual variance
set traits tlocs
simulate [chromosome] markers
simulate markers
simulate tloc
simulate 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
use exact summation for trait
use full EM
use locus-by-locus sampling for setup
use MC realizations for trait
use MC summation for trait
use MCEM and SA for maximization
use multiplier MC realizations for null
use partitioned EM
use sequential imputation for setup
use sequential imputation realizations for setup