application_programs
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| application_programs [2016/09/30 19:31] – andres | application_programs [2018/06/20 20:12] – shogo | ||
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| 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. | ||
| - | **Most** of the programs now support being called with the parameter file as an argument, e.g. < | + | **Most** of the programs now support being called with the parameter file as an argument, e.g. < |
| - | Download {{:blupf90_all4.pdf|BLUP90 | + | Download {{:blupf90_all7.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 | ||
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| Available by request | Available by request | ||
| - | * 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) | ||
| * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above | * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above | ||
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| 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 |
| + | * CBLUP90MBE - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) with support for very large models for multi-breed evaluations | ||
| * [[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 |
| * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
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application_programs.txt · Last modified: 2024/06/19 14:22 by andres