FAQ: examples, options, and tips for BLUPF90 family programs and modeling
Technical problems and segmentation fault
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System Error: Received a message like “The program can't start because libiomp5md.dll is missing…” in Windows.
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Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs
Data preparation program
REML
blupf90+: This is a combination of remlf90, airemlf90, and blupf90
Gibbs Sampler
OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed (known) variances
gibbsf90+: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
gibbs1f90: Faster than GIBBS2F90 without missing traits
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gibbs3f90: With heterogeneous residual variances
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thrgibbs3f90: Threshold + linear model with heterogeneous residual variances
Post-Gibbs Analysis
postgibbsf90: Statistics and graphics for convergence diagnosis and post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs). The graphs are created with gnuplot, which must be pre-installed.
BLUP
blupf90+: This is a combination of remlf90, airemlf90, and blupf90
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cblup90iod2: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions)
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blupf90: (G)BLUP with SOR, FSPAK or PCG
blup90iod2: (G)BLUP for a large number of equations (available only under some conditions)
blup90iod2r: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions)
blup90iod2hr: (G)BLUP with AIREMLF90-type heterogeneous residual variance for a large number of equations (available only under some conditions)
blup90mbe2: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, …
Accuracy (approximation)
accf90: Accuracy (reliability) for a large number of animals (available only under some conditions)
accf90GS: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options
accf90GS2: New accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options
Genomic Analysis
preGSf90: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS)
postGSf90: Post-analysis of genomic programs with options (GWAS)
predf90: Prediction of EBV using only SNP
qcf90 - a quality-control tool on genotypes and pedigree information
Additional programs
inbupgf90 - a program to calculate inbreeding coefficients with incomplete pedigree
seekparentf90 - a program to verify paternity and parent discovery using SNP markers
Modeling
* Sire model (cg: contemporary group)
y = μ + cg + ... + sire + e
y = μ + cg + ... + sire + MGS + e
where cg = common environment (farm, year, season, management, ...)
* Animal model (pe: permanent environment)
* Single record / animal
y = μ + cg + ... + animal + e
* Multiple records / animal
y = μ + cg + ... + animal + pe + e
* Random regressions f(t)
y = μ + cg + ... + f(t1) + f(t2)*animal + f(t3)*pe + e
where f(t) = a function of t (t: continuous variable)
* Maternal effect model (mpe: maternal permanent environment)
y = μ + cg + ... + animal + maternal + mpe + e