application_programs
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application_programs [2012/05/15 09:31] – andres | application_programs [2022/10/03 11:45] – dani | ||
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- | The programs support mixed models with multiple-correlated effects, multiple animal models and dominance. | + | The [[distribution|programs]] support mixed models with multiple-correlated effects, multiple animal models and dominance. |
- | * BLUPF90 - BLUP in memory | + | **Most** of the programs now support being called with the parameter file as an argument, e.g. < |
- | | + | |
- | | + | Download |
- | * AIREMLF90 | + | |
- | * | + | \\ |
- | * CBLUP90 | + | How to cite the BLUPF90 manual: |
- | * CBLUP90THR | + | Misztal I., Tsuruta S., Lourenco D.A.L., Aguilar I., Legarra A., and Vitezica Z. 2014. Manual for BLUPF90 family of programs. |
- | * CBLUP90REML | + | |
- | * GIBBSF90 | + | \\ |
- | * GIBBS1F90 - as above but faster because mixed model equations created only once | + | ===== Programs ===== |
- | * GIBBS2F90 - as above but with joint sampling of correlated effects | + | |
- | * | + | **Available for research (free)** |
- | * | + | * [[readme.blupf90plus|BLUPF90+]] |
- | * THRGIBBSF90 | + | * [[readme.gibbsf90plus|GIBBSF90+]] |
- | * THRGIBBS1F90 | + | * [[readme.postgibbs|POSTGIBBSF90]] |
- | * RENUMF90 | + | * [[Readme.Renumf90|RENUMF90]] |
+ | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships | ||
+ | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | ||
+ | * [[Readme.predictf90|PREDICTF90]] | ||
+ | * [[Readme.predf90|PREDF90]] | ||
+ | * [[readme.qcf90|QCF90]] | ||
+ | * [[Readme.Inbupgf90|INBUPGF90]] | ||
+ | * [[Readme.SeekParentf90|SEEKPARENTF90]] | ||
+ | |||
+ | /*Included in application programs*/ | ||
+ | |||
+ | **Available by request** | ||
+ | * QXPAK - joint analysis | ||
+ | * MRF90 - Method R program suitable | ||
+ | * COXF90 | ||
+ | * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) | ||
| | ||
- | + | **Available only under research agreement** | |
- | Available | + | * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta) |
- | * MRF90 - Method R program suitable | + | * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90) |
- | * COXF90 – Bayesian Cox model - contact Juan Pablo Sanchez | + | * [[readme.thr1pcg|CBLUP90IOD2]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) |
- | * BLUPF90HYP – BLUPF90 with hypothesis testing | + | * CBLUP90MBE |
+ | * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values | ||
+ | * [[readme.accgs|ACCF90GS]] | ||
+ | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations | ||
+ | * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
+ | * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP) | ||
+ | * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation | ||
+ | * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, | ||
| | ||
- | Available only under research agreement | + | **No longer updated (as of May 2022)** |
- | * BLUP90IOD | + | * [[readme.blupf90|BLUPF90]] |
- | * | + | * [[readme.reml|REMLF90]] - accelerated EM REML |
- | * ACCF90 | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances |
- | * BLUP90ADJ | + | * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic |
- | + | * [[readme.gibbs1|GIBBS1F90]] | |
- | Included in application programs | + | * [[readme.gibbs2|GIBBS2F90]] |
- | * | + | * [[readme.gibbs3|GIBBS3F90]] |
+ | * THRGIBBSF90 - Gibbs sampling for any combination | ||
+ | * [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified with several options (S. Tsuruta) | ||
+ | * [[readme.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits | ||
+ | * CBLUP90 | ||
+ | * CBLUP90THR | ||
+ | | ||
+ | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | ||
+ | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic | ||
+ | |||
+ | Other programming contributions were made by Miguel Perez-Enciso '' |
application_programs.txt · Last modified: 2024/07/22 14:35 by andres