The programs support mixed models with multiple-correlated effects, multiple animal models and dominance.

**Most** of the programs now support being called with the parameter file as an argument, e.g.

blupf90 renf90.par

. This avoids typing the name of the file in interactive or doing the trick

echo renf90.par | blupf90

.

Download BLUPF90 family manual. Note that some programs repertoried below are not in the manual (e.g. `inbupgf90`

)

- BLUPF90 - BLUP in memory
- REMLF90 - accelerated EM REML
- QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) QxPak web page
- AIREMLF90 - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta)
- 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 for creating mixed model equations only once
- GIBBS2F90 - as above but with joint sampling of correlated effects
- GIBBS3F90 - as above with support for heterogeneous residual variances
- GIBBS2CEN - support censored data (J. Arango)
- GIBBS2RECUR - support recursive models (J. P. Sanchez)
- POSTGIBBSF90 - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
- THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee)
- THRGIBBS1F90 - as above but simplified with several options (S. Tsuruta)
- RENUMF90 - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets
- INBUPGF90 - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar)
- SEEKPARENTF90 - a program to verify paternity and parent discovery using SNP markers (I. Aguilar)
- PREDICTF90 - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar)
- PREDF90 - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution

Available by request

- MRF90 - Method R program suitable for very large data sets; contact T. Druet.
- COXF90 – Bayesian Cox model - contact J. P. Sanchez (JuanPablo.Sanchez@irta.cat)
- BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above

Available only under research agreement

- BLUP90IOD2 - BLUP by iteration on data with PCG for very large models (S. Tsuruta)
- CBLUP90IOD - BLUP by iteration on data for threshold-linear models
- ACCF90 - approximation of accuracies for breeding values
- BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations
- BLUP90ADJ - BLUP data preadjustment tool

Included in application programs

- PREGSF90 – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar)
- POSTGSF90 – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar)

Other programming contributions were made by Miguel Perez-Enciso `(user_file)`

and François Guillaume (Jenkins hashing functions).