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FAQ: examples and options for BLUPF90 family programs

Download BLUPF90 manual

Technical problems and segmentation fault

Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs

Data preparation program

REML

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

  • 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
  • gibbsf90test: This is a beta version for a combined Gibbs program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90

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: (G)BLUP with SOR, FSPAK or PCG
  • predictf90: Calculates y-hat
  • 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)
  • cblup90iod2: (G)BLUP with threshold + linear model 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

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
faq.txt · Last modified: 2019/03/28 19:48 by yutaka