application_programs
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| application_programs [2012/05/10 19:51] – created ignacy | application_programs [2018/06/20 20:46] – shogo | ||
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| - | The 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. |
| - | * BLUPF90 - BLUP in memory | + | **Most** of the programs now support being called with the parameter file as an argument, e.g. < |
| - | | + | |
| - | | + | Download {{: |
| - | * AIREMLF90 - Average Information REML (S. Tsuruta) | + | |
| - | * AIREMLRES | + | * [[readme.blupf90|BLUPF90]] - BLUP in memory |
| - | * CBLUP90 | + | |
| - | * CBLUP90THR | + | |
| - | * | + | * CBLUP90 |
| - | * GIBBSF90 - simple block implementation of Gibbs sampling | + | * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray) |
| - | * GIBBS1F90 - as above but faster | + | * CBLUP90REML - as above but with quasi REML (B. Auvray) |
| - | * GIBBS2F90 - as above but with joint sampling of correlated effects | + | * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling |
| - | * GIBBS3F90 - as above with support for heterogeneous residual variances | + | * [[readme.gibbs1|GIBBS1F90]] - as above but faster |
| - | * POSTGIBBSF90 - graphical tool for post-Gibbs analysis (S. Tsuruta) | + | * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects |
| - | * THRGIBBSF90 - Gibbs -sampling for any combination of categorical and linear traits (D. Lee) | + | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances |
| - | * THRGIBBS1F90 | + | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic |
| - | * RENUMF90 - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets | + | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic |
| - | | + | * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics |
| + | * THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) - no genomic | ||
| + | * [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified | ||
| + | * [[Readme.Renumf90|RENUMF90]] - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets | ||
| + | | ||
| + | * [[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 | ||
| - | * | + | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// |
| - | * COXF90 – Bayesian Cox model - contact | + | * MRF90 - Method R program suitable for a large data set; contact |
| - | * BLUPF90HYP – BLUPF90 with hypothesis testing | + | * COXF90 – Bayesian Cox model - contact |
| + | * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact | ||
| | | ||
| Available only under research agreement | Available only under research agreement | ||
| - | * BLUP90IOD | + | * [[readme.pcg2|BLUP90IOD2]] |
| - | * | + | * BLUP90IOD2R & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances |
| - | * ACCF90 - approximation of multiple-trait accuracies | + | * [[readme.thr1pcg|CBLUP90IOD]] |
| - | * BLUP90ADJ - Data preadjustment tool | + | * 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.accgs|ACCF90GS]] | ||
| + | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra) | ||
| + | * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
| + | * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2R, | ||
| | | ||
| Included in application programs | Included in application programs | ||
| - | * | + | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) |
| + | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | ||
| + | |||
| + | Other programming contributions were made by Miguel Perez-Enciso '' | ||
application_programs.txt · Last modified: 2024/06/19 14:22 by andres