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BLUPF90 Family of Programs
now with support for genomic selection
Ignacy Misztal and collaborators, University of Georgia BLUPF90 family of programs is a collection of software in Fortran 90/95 for mixed model computations in animal breeding. The goal of the software is to be as simple as with a matrix package and as efficient as in a programming language. For general description, see a paper from the CCB'99 workshop or see a paper on BGF90 at 7th WCGALP.
For variance component estimation, the family offers choices for simple and complicated models; see paper “Reliable computing in estimation of variance components”. From 2009 the programs are successively modified for genomic selection using a single-step approach (or ssGBLUP) by Ignacio Aguilar and Shogo Tsuruta.
Headline
FAQ for BLUPF90 programs Input files
data pedigree
Data preparation program
renumf90 (ver 1.92) read me examples
Frequent mistakes in a parameter file for BLUPF90 programs
parameter files for various models examples
REML
remlf90 (ver 1.76) read me: EM algorithm - PDF airemlf90 (ver 1.99) read me: Average Information REML + REMLF90 - Standard Errors (PDF)
Gibbs sampling OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed variances
gibbs1f90 (ver 1.42) read me: Faster than GIBBS2F90 without missing traits gibbs2f90 (ver 1.76) read me gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model
Post-Gibbs Analysis
postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs)
BLUP
blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations (available only under some conditions)
Accuracy
accf90 : (ver 1.63) read me: Accuracy (reliability) for a large number of animals (available only under some conditions)
Genomic Analysis
preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs