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FAQ: examples, options, and tips for BLUPF90 family programs and modeling

Download BLUPF90 manual

Technical problems and segmentation fault

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
  • gibbs2f90: Useful with missing traits
  • gibbs3f90: With heterogeneous residual variances
  • thrgibbs1f90: Threshold + linear model
  • 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
  • blup90iod3 (new blup90iod) - a combined program of blup90iod2, blu90iod2r, blup90iod2hr, and blup90mbe2 with new features
  • cblup90iod2: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions)
  • predictf90: Calculates y-hat
  • 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
  • validationf90 - a program to validate models
  • probcatf90 - a program to transform solutions from linear or threshold model to probabilities

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
faq.txt · Last modified: 2024/10/23 21:56 by shogo

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