application_programs
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application_programs [2012/05/15 09:31] – andres | application_programs [2016/09/30 19:31] – 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 | + | **Most** of the programs now support being called with the parameter file as an argument, e.g. < |
- | | + | |
- | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) | + | Download |
- | * AIREMLF90 - Average Information REML (S. Tsuruta) | + | |
- | * AIREMLRES | + | |
- | * CBLUP90 | + | * [[readme.reml|REMLF90]] - accelerated EM REML |
- | * CBLUP90THR | + | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) |
- | * | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) |
+ | * 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 | + | * [[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 |
- | | + | |
+ | * [[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 | ||
- | * | + | * 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]] |
- | * | + | * [[readme.thr1pcg|CBLUP90IOD]] |
- | * ACCF90 - approximation of multiple-trait | + | * [[readme.acc|ACCF90]] - approximation of accuracies |
- | * 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|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