application_programs
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application_programs [2018/06/20 20:23] – shogo | application_programs [2022/05/06 01:54] – dani | ||
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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 {{: | Download {{: | ||
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* 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) - no genomic | * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic | ||
- | * GIBBSF90 - simple block implementation of Gibbs sampling - no genomic | + | * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic |
* [[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 | ||
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* THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) - no genomic | * 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.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits | ||
* [[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) | * [[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) | + | * [[Readme.pedictf90|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 | * PREDF90 - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution | ||
- | * BLUPF90TEST | + | * [[readme.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information |
- | * GIBBSF90TEST (new GIBBSF90) - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, | + | * [[readme.blupf90new|BLUPF90+]] |
+ | * [[readme.gibbsf90new|GIBBSF90+]] - a combined program of gibbs1f90, | ||
Available by request | Available by request | ||
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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) | ||
- | * BLUP90IOD2R | + | * BLUP90IOD2RR |
- | * [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) | + | * [[readme.thr1pcg|CBLUP90IOD2]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) |
* 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 | * 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 | ||
+ | * [[readme.accgs|ACCF90GS]] - approximation of accuracies for genomic breeding values | ||
* BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra) | * 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.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
- | * BLUP90IODTEST (new BLUP90IOD) - a combined program of BLUP90IOD2, | + | * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP) |
+ | * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation | ||
+ | * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, | ||
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Included in application programs | Included in application programs |
application_programs.txt · Last modified: 2024/07/22 14:35 by andres