BLUPF90 family of programs

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.

The family contains:

Modules

• SPARSEM - sparse matrix manipulation
• SPARSEOP - sparse matrix operations including factorization and inversion
• DENSEOP - dense matrix operations (T. Strabel)
• PROB - probability routines for use in threshold models and Gibbs sampling
• GIBBS - operations useful for data manipulation in Gibbs sampling 

Application programs

They support mixed models with multiple-correlated effects, multiple animal models and dominance. See comments on properties of some of the programs here and this link (will) contain examples of parameter files.

• BLUPF90 - BLUP in memory
• REMLF90 - accelerated EM REML
• QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso)
• AIREMLF90 - Average Information REML (S. Tsuruta)
• AIREMLRES - as above with support for heterogeneous residual variances (T. Druet)
• CBLUP90  - Solutions for bivariate linear-threshold models
• CBLUP90THR  -as above but with thresholds computed and many linear traits (B. Auvray)
• CBLUP90REML - as above but with quasi REML (B. Auvray)
• GIBBSF90 - simple block implementation of Gibbs sampling
• GIBBS1F90 - as above but faster because mixed model equations created only once
• GIBBS2F90 - as above but with joint sampling of correlated effects
• GIBBS3F90 - as above with support for heterogeneous residual variances
• POSTGIBBSF90 - graphical tool for post-Gibbs analysis (S. Tsuruta)
• THRGIBBSF90 - Gibbs -sampling for any combination of categorical and linear traits (D. Lee)
• THRGIBBS1F90 – As above but simplified (S. Tsuruta)

Under development

• GIBBSCF90 - As gibbs2f90 but with support for right censoring (J. Arango)

Available by request

• MRF90 - Method R program suitable for very large data sets; contact Tom Druet.

Available only under research agreement

• BLUP90IOD - BLUP by iteration on data with support for very large problems (S. Tsuruta)
• BLUP90IODTHR - as above for for threshold-linear models
• ACCF90 - approximation of multiple-trait accuracies
• BLUP90ADJ - Data preadjustment tool

Most programs are available as a package for download and compilation on Unix systems. Linux binaries and Windows executables are available for some programs but they may be out of date. The package is updated often so check file Changes on the latest changes.

All programs use renumbered data and therefore may be hard to use for those with little knowledge about mixed models. A renumbering program specific for this package is renumf90;  Its binaries  under Linux are available.  Alternatively, one can use renummat3.f available in the renum directory under old programs.

If some programs return strange messages and do not finish, please read about compilation problems.