application_programs
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| application_programs [2018/03/06 21:10] – shogo | application_programs [2018/03/06 21:43] – shogo | ||
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| * [[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) | + | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) |
| - | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) | + | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) |
| * [[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 | ||
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| 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) | ||
application_programs.txt · Last modified: 2024/06/19 14:22 by andres