application_programs
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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
- 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)
- BLUPF90TEST (new BLUPF90) - a combined program of blupf90, remlf90, and airemlf90: under test
- GIBBSF90TEST (new GIBBSF90) - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90: under test
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)
- BLUP90ADJ - BLUP data preadjustment tool
- DEPROOFSF90 - computation of deregressed proof (DRP)
- DYDF90 - computation of daughter yield deviation (DYD) known as progeny trait deviation
- BLUP90IODTEST (new BLUP90IOD) - a combined program of BLUP90IOD2, BLUP90IOD2R, and BLUP90IOD2HR: under test
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).
application_programs.1559780562.txt.gz · Last modified: 2024/03/25 18:22 (external edit)