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
)
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AIREMLF90 - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta)
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
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
GIBBS2CEN - support censored data (J. Arango) - no genomic
GIBBS2RECUR - support recursive models (J. P. Sanchez) - no genomic
POSTGIBBSF90 - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
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
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
QCF90 - a quality-control tool on genotypes and pedigree information (Y. Masuda)
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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)
BLUP90IOD2R & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances
CBLUP90IOD - 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
BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra)
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DYDF90 - computation of daughter yield deviation (DYD) known as progeny trait deviation
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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).