BLUPF90

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 shown below are not in the manual (e.g. inbupgf90)

How to cite the BLUPF90 manual: Misztal I., Tsuruta S., Lourenco D.A.L., Aguilar I., Legarra A., and Vitezica Z. 2014. Manual for BLUPF90 family of programs.

Programs

Available for research (free with restriction: # genotyped animals = 25,000)

BLUPF90+ - a combined program of blupf90, remlf90, and airemlf90
GIBBSF90+ - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
POSTGIBBSF90 - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
RENUMF90 - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets
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)
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
QCF90 - a quality-control tool on genotypes and pedigree information (Y. Masuda)
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)
VALIDATIONF90 - a program to perform validation of predictions (coming soon!)
RRMEBVF90 - postprocessor for random regression models

Available by request

QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) QxPak web page
MRF90 - Method R program suitable for a large data set; 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)
BLUP90IOD3 (new BLUP90IOD) - a combined program of BLUP90IOD2, BLUP90IOD2RR, BLUP90IOD2HR, and BLUP90MBE2 with new features
CBLUP90IOD2 - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits)
CBLUP90MBE - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) with support for very large models for multi-breed evaluations
ACCF90 - approximation of accuracies for breeding values
ACCF90GS - approximation of accuracies for genomic breeding values based on diagonals of G
ACCF90GS2 - new approximation of accuracies for genomic breeding values based on block sparse inversion
BLUP90ADJ - BLUP data preadjustment tool
DEPROOFSF90 - computation of deregressed proof (DRP)
DYDF90 - computation of daughter yield deviation (DYD) known as progeny trait deviation

No longer updated and obsolete (as of May 2022)

BLUPF90 - BLUP in memory
REMLF90 - accelerated EM REML
AIREMLF90 - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta)
GIBBSF90 - simple block implementation of Gibbs sampling - no genomic
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
THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) - no genomic
THRGIBBS1F90 - as above but simplified with several options (S. Tsuruta)
THRGIBBS3F90 - as above with heterogeneous residual variances for linear traits
CBLUP90 - solutions for bivariate linear-threshold models (works only for 2 trait model: threshold and linear)
CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray)
CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic
GIBBS2CEN - support censored data (J. Arango) - no genomic
GIBBS2RECUR - support recursive models (J. P. Sanchez) - no genomic
BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90)
BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra)

Other programming contributions were made by Miguel Perez-Enciso (user_file) and François Guillaume (Jenkins hashing functions).