application_programs
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| application_programs [2012/05/15 09:31] – andres | application_programs [2012/07/24 10:44] – andres | ||
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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 {{blupf90.pdf}} | + | |
| - | | + | * [[readme.blupf90|BLUPF90]] - BLUP in memory {{blupf90.pdf}} |
| - | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) | + | |
| - | * AIREMLF90 - Average Information REML (S. Tsuruta) | + | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) |
| - | * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances |
| - | * CBLUP90 | + | * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) |
| - | * CBLUP90THR | + | * CBLUP90 |
| - | * | + | * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray) |
| + | * CBLUP90REML - as above but with quasi REML (B. Auvray) | ||
| * GIBBSF90 - simple block implementation of Gibbs sampling | * GIBBSF90 - simple block implementation of Gibbs sampling | ||
| - | * GIBBS1F90 - as above but faster | + | * [[readme.gibbs1|GIBBS1F90]] - as above but faster |
| - | * GIBBS2F90 - as above but with joint sampling of correlated effects | + | * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects |
| - | * GIBBS3F90 - as above with support for heterogeneous residual variances | + | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances |
| - | * POSTGIBBSF90 - graphical tool for post-Gibbs analysis (S. Tsuruta) | + | * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics |
| - | * THRGIBBSF90 - Gibbs -sampling for any combination of categorical and linear traits (D. Lee) | + | * THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) |
| - | * THRGIBBS1F90 – As above but simplified (S. Tsuruta) | + | * [[readme.thrgibbs1|THRGIBBS1F90]] – as above but simplified |
| - | * RENUMF90 - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets | + | * [[Readme.Renumf90|RENUMF90]] - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets |
| | | ||
| Available by request | Available by request | ||
| - | * | + | * MRF90 - Method R program suitable for very large data sets; contact |
| - | * COXF90 – Bayesian Cox model - contact | + | * COXF90 – Bayesian Cox model - contact |
| - | * BLUPF90HYP – BLUPF90 with hypothesis testing | + | * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact |
| | | ||
| Available only under research agreement | Available only under research agreement | ||
| - | * BLUP90IOD | + | * [[readme.pcg2|BLUP90IOD2]] |
| - | * BLUP90IODTHR - as above for threshold-linear models | + | * [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models |
| - | * ACCF90 - approximation of multiple-trait | + | * BLUP90IODTHR - as above for threshold-linear models |
| - | * BLUP90ADJ - Data preadjustment tool | + | * [[readme.acc|ACCF90]] - approximation of accuracies |
| + | * BLUP90ADJ - data preadjustment tool | ||
| | | ||
| Included in application programs | Included in application programs | ||
| - | * | + | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres