application_programs
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application_programs [2014/04/09 16:31] – shogo | application_programs [2018/06/20 20:28] – 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. < | ||
- | * [[readme.blupf90|BLUPF90]] - BLUP in memory | + | Download {{: |
- | * [[readme.reml|REMLF90]] - accelerated EM REML {{remlf90.pdf}} | + | |
- | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | + | * [[readme.blupf90|BLUPF90]] - BLUP in memory |
- | | + | * [[readme.reml|REMLF90]] - accelerated EM REML |
- | * CBLUP90 | + | * [[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) | * 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]] | + | * [[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.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar) | * [[Readme.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar) | ||
+ | * [[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 | ||
+ | * [[readme.blupf90new|BLUPF90TEST (new BLUPF90)]] - a combined program of blupf90, remlf90, and airemlf90: under test | ||
+ | * [[readme.gibbsf90new|GIBBSF90TEST (new GIBBSF90)]] - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, | ||
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 | ||
| | ||
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 | + | * BLUP90IOD2R & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances |
+ | * [[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 | ||
+ | * BLUP90IODTEST (new BLUP90IOD) - a combined program of BLUP90IOD2, BLUP90IOD2R, | ||
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Included in application programs | Included in application programs |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres