application_programs
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application_programs [2012/05/28 14:28] – shogo | application_programs [2016/10/03 16:58] – 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. |
- | FIXME Should we link all programs | + | **Most** of the programs |
- | * [[readme.blupf90|BLUPF90]] - BLUP in memory | + | Download {{: |
- | * [[readme.reml|REMLF90]] - accelerated EM REML {{remlf90.pdf}} | + | |
+ | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
+ | * [[readme.reml|REMLF90]] - accelerated EM REML | ||
* QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | ||
- | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including heterogeneous residual variances (S. Tsuruta) | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including |
- | * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) | + | |
* CBLUP90 | * CBLUP90 | ||
* CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray) | * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray) | ||
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* [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta) | * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta) | ||
* 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) | ||
- | * [[readme.thrgibbs1|THRGIBBS1F90]] | + | * [[readme.thrgibbs1|THRGIBBS1F90]] |
* [[Readme.Renumf90|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 | ||
- | | + | |
+ | * [[Readme.SeekParentf90|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 | ||
Available by request | Available by request | ||
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Available only under research agreement | Available only under research agreement | ||
- | * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with support | + | * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta) |
* [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models | * [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models | ||
- | * BLUP90IODTHR - as above for threshold-linear models | ||
* [[readme.acc|ACCF90]] - approximation of accuracies for breeding values | * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values | ||
- | * BLUP90ADJ - data preadjustment tool | + | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations |
+ | * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
| | ||
Included in application programs | Included in application programs | ||
* [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) | * [[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) | ||
+ | |||
+ | Other programming contributions were made by Miguel Perez-Enciso '' |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres