application_programs
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| application_programs [2022/05/10 21:23] – dani | application_programs [2023/09/04 20:56] – [Programs] shogo | ||
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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 {{: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. '' |
| \\ | \\ | ||
| - | **Programs available | + | :!: 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 | ||
| * [[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, | ||
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| * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar) | * [[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) | * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar) | ||
| - | * [[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) | ||
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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) | ||
| - | * 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 |
| | | ||
| **No longer updated (as of May 2022)** | **No longer updated (as of May 2022)** | ||
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| * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic | ||
| * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - 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