application_programs
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application_programs [2022/05/06 17:56] – dani | application_programs [2022/05/10 20:30] – dani | ||
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**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 {{: |
* [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | ||
- | * [[readme.blupf90new|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | + | * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, |
- | * [[readme.gibbsf90new|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, | + | |
- | * CBLUP90 | + | |
- | * 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 | ||
* [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | ||
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* [[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) | ||
* [[Readme.pedictf90|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 | + | * [[Readme.predf90|PREDF90]] - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution |
* [[readme.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information (Y. Masuda) | * [[readme.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information (Y. Masuda) | ||
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* [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | ||
- | Deprecated programs | + | Deprecated programs |
* [[readme.blupf90|BLUPF90]] - BLUP in memory | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
* [[readme.reml|REMLF90]] - accelerated EM REML | * [[readme.reml|REMLF90]] - accelerated EM REML | ||
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* [[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.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits | ||
+ | * CBLUP90 | ||
+ | * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray) | ||
Other programming contributions were made by Miguel Perez-Enciso '' | Other programming contributions were made by Miguel Perez-Enciso '' |
application_programs.txt · Last modified: 2024/06/19 14:22 by andres