application_programs
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application_programs [2012/05/15 09:33] – andres | application_programs [2022/05/10 20:30] – 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. |
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+ | **Most** of the programs now support being called with the parameter file as an argument, e.g. < | ||
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+ | Download {{: | ||
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+ | * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | ||
+ | * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, | ||
+ | * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic | ||
+ | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | ||
+ | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic | ||
+ | * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta) | ||
+ | * [[Readme.Renumf90|RENUMF90]] - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets | ||
+ | * [[Readme.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar) | ||
+ | * [[Readme.SeekParentf90|SEEKPARENTF90]] - a program to verify paternity and parent discovery using SNP markers (I. Aguilar) | ||
+ | * [[Readme.pedictf90|PREDICTF90]] - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar) | ||
+ | * [[Readme.predf90|PREDF90]] - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution | ||
+ | * [[readme.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information (Y. Masuda) | ||
- | * BLUPF90 - BLUP in memory {{blupf90.pdf}} | ||
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- | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | ||
- | * AIREMLF90 - Average Information REML (S. Tsuruta) | ||
- | * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) | ||
- | * CBLUP90 | ||
- | * CBLUP90THR | ||
- | * | ||
- | * GIBBSF90 - simple block implementation of Gibbs sampling | ||
- | * GIBBS1F90 - as above but faster because mixed model equations created only once | ||
- | * GIBBS2F90 - as above but with joint sampling of correlated effects | ||
- | * GIBBS3F90 - as above with support for heterogeneous residual variances | ||
- | * POSTGIBBSF90 - graphical tool for post-Gibbs analysis (S. Tsuruta) | ||
- | * THRGIBBSF90 - Gibbs -sampling for any combination of categorical and linear traits (D. Lee) | ||
- | * THRGIBBS1F90 – As above but simplified (S. Tsuruta) | ||
- | * RENUMF90 - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets | ||
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Available by request | Available by request | ||
- | * | + | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// |
- | * COXF90 – Bayesian Cox model - contact | + | * MRF90 - Method R program suitable for a large data set; contact |
- | * BLUPF90HYP – BLUPF90 with hypothesis testing | + | * COXF90 – Bayesian Cox model - contact |
+ | * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact | ||
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Available only under research agreement | Available only under research agreement | ||
- | * BLUP90IOD | + | * [[readme.pcg2|BLUP90IOD2]] |
- | * | + | * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90) |
- | * ACCF90 - approximation of multiple-trait accuracies | + | * [[readme.thr1pcg|CBLUP90IOD2]] |
- | * BLUP90ADJ - Data preadjustment tool | + | * 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 |
+ | * [[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 (A. Legarra) | ||
+ | * [[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, | ||
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Included in application programs | Included in application programs | ||
- | * | + | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) |
+ | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | ||
+ | |||
+ | Deprecated programs (as of May 2022) | ||
+ | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
+ | * [[readme.reml|REMLF90]] - accelerated EM REML | ||
+ | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) | ||
+ | * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic | ||
+ | * [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once | ||
+ | * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects | ||
+ | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances | ||
+ | * THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) - no genomic | ||
+ | * [[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 - as above but with thresholds computed and many linear traits (B. Auvray) | ||
+ | |||
+ | Other programming contributions were made by Miguel Perez-Enciso '' |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres