application_programs
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
application_programs [2016/05/12 14:14] – dani | application_programs [2018/03/13 21:31] – dani | ||
---|---|---|---|
Line 1: | Line 1: | ||
The [[distribution|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. | ||
- | Download {{:blupf90_all4.pdf|BLUP90 | + | **Most** of the programs now support being called with the parameter file as an argument, e.g. < |
+ | |||
+ | Download {{:blupf90_all6.pdf|BLUPF90 family | ||
* [[readme.blupf90|BLUPF90]] - BLUP in memory | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
* [[readme.reml|REMLF90]] - accelerated EM REML | * [[readme.reml|REMLF90]] - accelerated EM REML | ||
- | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) |
- | | + | * 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) | + | * CBLUP90REML - as above but with quasi REML (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 | + | |
* [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once | * [[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.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects | ||
* [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances | ||
+ | * [[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.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) - no genomic |
* [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified with several options (S. Tsuruta) | * [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified with several options (S. Tsuruta) | ||
* [[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 | ||
Line 24: | Line 27: | ||
Available by request | Available by request | ||
+ | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | ||
* MRF90 - Method R program suitable for very large data sets; contact T. Druet. | * MRF90 - Method R program suitable for very large data sets; contact T. Druet. | ||
* COXF90 – Bayesian Cox model - contact J. P. Sanchez (JuanPablo.Sanchez@irta.cat) | * COXF90 – Bayesian Cox model - contact J. P. Sanchez (JuanPablo.Sanchez@irta.cat) | ||
Line 30: | Line 34: | ||
Available only under research agreement | Available only under research agreement | ||
* [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta) | * [[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 |
* [[readme.acc|ACCF90]] - approximation of accuracies for breeding values | * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values | ||
* BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres