allow pedigree size
assign gender
pedcheck
assume all observed
genedrop
check eigenvalue computation
multivar
check eigenvalues
check ginverse
check gmatrix
check progress MC iterations
check trace
component compute two-locus inbreeding coefficient
kin
compute component inbreeding coefficient
compute component kinship coefficient
compute eigenvalues
compute inbreeding coefficient
compute kinship coefficient
compute scores every iterations
compute two-locus inbreeding coefficient
fit additive correlations
fit additive covariances
fit environmental model
fit residual correlations
fit residual covariances
ignore gender
input eigenvalue file
input marker data file
input pedigree file
input pedigree record father mother
input pedigree record gender absent
input pedigree record gender present
input pedigree record mother father
input pedigree record names 3
input pedigree record names 3 integers
input pedigree record names 3 integers reals
input pedigree record observed absent
input pedigree record observed present
input pedigree record traits integers
input pedigree size
input seed file
limit breeding iterations
limit EM iterations
map chromosome gender marker distance
map chromosome gender marker positions
map chromosome gender marker recombination fractions
map chromosome gender trait all interval proportions
map chromosome gender trait beginning distance
map chromosome gender trait beginning recombination fractions
map chromosome gender trait ending distance
map chromosome gender trait ending recombination fractions
map chromosome gender trait external distance
map chromosome gender trait external recombination fractions
map chromosome gender trait intervals proportions
map chromosome gender traits marker distances
map chromosome gender traits marker recombination fractions
map chromosome marker distances
map chromosome marker positions
map chromosome marker recombination fractions
map chromosome trait all interval proportions
map chromosome trait beginning distance
map chromosome trait beginning recombination fractions
map chromosome trait ending distance
map chromosome trait ending recombination fractions
map chromosome trait external distance
map chromosome trait external recombination fractions
map chromosome trait intervals proportions
map chromosome traits marker distances
map chromosome traits marker recombination fractions
map gender marker distances
map gender marker positions
map gender marker recombination fractions
map gender trait all interval proportions
map gender trait beginning distance
map gender trait beginning recombination fractions
map gender trait ending distance
map gender trait ending recombination fractions
map gender trait external distance
map gender trait external recombination fractions
map gender trait intervals proportions
map gender traits marker distances
map gender traits marker recombination fractions
map marker distances
map marker positions
map marker recombination fractions
map trait all interval proportions
map trait beginning distance
map trait beginning recombination fractions
map trait ending distance
map trait ending recombination fractions
map trait external distance
map trait external recombination fractions
map trait intervals proportions
map traits marker distances
map traits marker recombination fractions
output final adjusted phenotypes
output marker seeds only
output pedigree chronological
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 score file
output seed file
output spacing EM iterations
output statistics correlations
output statistics covariances
output trait seeds only