allow component size
allow observed individuals
allow pedigree size
assign gender
pedcheck
assume all observed
genedrop
check eigenvalue computation
multivar
check eigenvalues
check ginverse
check gmatrix
check marker consistency [only]
check progress MC iterations
check trace
compute [component] inbreeding coefficient
kin
compute [component] kinship coefficient
compute [component] two-locus inbreeding coefficient
compute eigenvalues
compute estimates I times
lm_map
compute ibd statistics
lm_ibdtests
civil
compute likelihood-ratio statistics
compute scores every iterations
fit additive correlations
fit additive covariances
fit environmental model
fit residual correlations
fit residual covariances
ignore gender
input eigenvalue file
input extra file
input gamete data file
input genotypes as rows
input haplotypes as columns of SNPs
input haplotypes as rows of SNPs
input individuals file
input individuals record names traits reals
input marker data file
input pedigree file
input pedigree record (father mother | father mother)
input pedigree record gender (present | absent)
input pedigree record inheritance integer pairs
markerdrop
input pedigree record names 3 [integers] [reals]
input pedigree record observed (absent | present)
input pedigree record traits integers
input pedigree record traits reals
input pedigree size
input rescue file
input seed file
limit breeding iterations
limit EM iterations
limit recombination fractions L
map [chromosome] test tlocs jointly at markers
map [chromosome] marker positions base pairs
map [chromosome] test tloc at markers
map [chromosome][gender] marker [Kosambi] distances
map [chromosome][gender] marker [Kosambi] positions
map [chromosome][gender] marker recombination fractions
map [chromosome][gender] test tloc all interval proportions
map [chromosome][gender] test tloc beginning [Kosambi] distance
map [chromosome][gender] test tloc beginning recombination fractions
map [chromosome][gender] test tloc ending [Kosambi] distance
map [chromosome][gender] test tloc ending recombination fractions
map [chromosome][gender] test tloc external distance
map [chromosome][gender] test tloc external Kosambi distance
map [chromosome][gender] test tloc external recombination fractions
map [chromosome][gender] test tloc intervals proportions
map [chromosome][gender] tlocs marker [Kosambi] distances
map [chromosome][gender] tlocs marker [Kosambi] positions
map [chromosome][gender] tlocs marker recombination fractions
map [gender] marker [Kosambi] distance
map [gender] marker [Kosambi] position
map [gender] marker recombination fraction
map [gender] tlocs marker [Kosambi] distance
map [gender] tlocs marker recombination fraction
map test tlocs no default external positions
map test tlocs no default interval proportions
map tlocs unlinked
ibddrop
output [overwrite] extra file
output [overwrite] individuals file
output [overwrite] pedigree file
output [overwrite] score file
output [overwrite] seed file
output all genotypes
output final adjusted phenotypes
output final generation
output founder genome labels
output four-gamete state order jacquard
output genotypes
output haplotype labels
output haplotypes as columns
output haplotypes as rows
output maps gender [averaged] [specific]
output marker seeds only
output meiosis indicators
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 permutation seeds only
output Rao-Blackwellized estimates file
output rescue data iterations
output rescue file
output sampler seeds only
output scores at markers
output scores every scored MC iterations
output seed file
output spacing EM iterations
output statistics correlations
output statistics covariances
output trait seeds only
output with spaces