application_programs
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| application_programs [2012/05/28 01:01] – ignacio | application_programs [2012/05/28 14:27] – shogo | ||
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| FIXME Should we link all programs to their Readme' | FIXME Should we link all programs to their Readme' | ||
| - | * BLUPF90 - BLUP in memory {{blupf90.pdf}} | + | |
| - | * REMLF90 - accelerated EM REML {{remlf90.pdf}} | + | |
| * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | ||
| - | * AIREMLF90 - Average Information REML with several options including heterogeneous residual variances (S. Tsuruta) | + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including heterogeneous residual variances (S. Tsuruta) |
| * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) | * AIREMLRES - as above with support for heterogeneous residual variances (T. Druet) | ||
| * CBLUP90 | * CBLUP90 | ||
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| * 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 | ||
| - | * 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 |
| - | * 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 - 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) | ||
| - | * 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 only under research agreement | Available only under research agreement | ||
| - | * BLUP90IOD2 - BLUP by iteration on data with support for very large models (S. Tsuruta) | + | * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with support for very large models (S. Tsuruta) |
| - | * CBLUP90IOD - BLUP by iteration on data for threshold-linear models | + | * [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models |
| * BLUP90IODTHR - as above for threshold-linear models | * BLUP90IODTHR - as above for threshold-linear models | ||
| - | * ACCF90 - approximation of accuracies for breeding values | + | * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values |
| * BLUP90ADJ - data preadjustment tool | * BLUP90ADJ - data preadjustment tool | ||
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| Included in application programs | Included in application programs | ||
| - | * | + | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres