application_programs
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
application_programs [2022/05/10 16:02] – dani | application_programs [2024/03/25 18:22] – external edit 127.0.0.1 | ||
---|---|---|---|
Line 3: | Line 3: | ||
**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 {{:blupf90_all7.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. '' | + | Download {{:blupf90_all8.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. '' |
+ | \\ | ||
+ | :!: How to cite the BLUPF90 manual: | ||
+ | Misztal I., Tsuruta S., Lourenco D.A.L., Aguilar I., Legarra A., and Vitezica Z. 2014. Manual for BLUPF90 family of programs. | ||
+ | |||
+ | \\ | ||
+ | ===== Programs ===== | ||
+ | |||
+ | **Available for research (free with restriction: | ||
* [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 | ||
* [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, | * [[readme.gibbsf90plus|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 | ||
- | * [[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) | ||
* [[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 | + | * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree |
- | * [[Readme.SeekParentf90|SEEKPARENTF90]] - a program to verify paternity and parent discovery using SNP markers | + | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts |
- | * [[Readme.pedictf90|PREDICTF90]] - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar) | + | * [[Readme.predictf90|PREDICTF90]] - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar) |
* [[Readme.predf90|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) | ||
+ | * [[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) | ||
+ | |||
+ | /*Included in application programs*/ | ||
- | Available by request | + | **Available by request** |
* QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http:// | ||
* MRF90 - Method R program suitable for a large data set; contact T. Druet. | * MRF90 - Method R program suitable for a large data set; contact T. Druet. | ||
Line 26: | Line 33: | ||
* 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 PCG for very large models (S. Tsuruta) | * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta) | ||
- | * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90) | ||
* [[readme.thr1pcg|CBLUP90IOD2]] - 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 | * [[readme.accgs|ACCF90GS]] - approximation of accuracies for genomic breeding values | ||
- | * BLUP90MBE | + | * [[readme.accgs2|ACCF90GS2]] |
* [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool | ||
* [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP) | * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP) | ||
* [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation | * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation | ||
- | * [[readme.pcgtest|BLUP90IODTEST | + | * [[readme.pcgtest|BLUP90IOD3 |
| | ||
- | Included in application programs | + | **No longer updated |
- | | + | |
- | | + | |
- | + | ||
- | 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 | ||
Line 54: | Line 56: | ||
* [[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) | ||
+ | * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic | ||
+ | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | ||
+ | * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic | ||
+ | * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90) | ||
+ | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra) | ||
+ | |||
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