application_programs
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| application_programs [2019/06/06 00:23] – dani | application_programs [2024/04/17 17:18] – andres | ||
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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 | + | Download {{:blupf90_all8.pdf|BLUPF90 family manual}}. Note that some programs |
| - | * [[readme.blupf90|BLUPF90]] - BLUP in memory | + | \\ |
| - | * [[readme.reml|REMLF90]] - accelerated EM REML | + | How to cite the BLUPF90 |
| - | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML | + | Misztal I., Tsuruta S., Lourenco D.A.L., Aguilar I., Legarra A., and Vitezica Z. 2014. Manual for BLUPF90 family of programs. |
| - | * CBLUP90 | + | |
| - | | + | \\ |
| - | | + | ===== Programs ===== |
| - | * [[readme.gibbs|GIBBSF90]] - simple block implementation | + | |
| - | * [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once | + | **Available |
| - | * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling | + | * [[readme.blupf90plus|BLUPF90+]] - a combined program |
| - | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances | + | * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program |
| - | * [[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) | ||
| - | * 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.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.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.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.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.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) | ||
| - | * [[Readme.pedictf90|PREDICTF90]] - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar) | + | * [[Readme.validationf90|VALIDATIONF90]] - a program to perform forward validation of predictions |
| - | * 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) | + | /*Included in application programs*/ |
| - | * [[readme.blupf90new|BLUPF90TEST (new BLUPF90)]] - a combined program of blupf90, remlf90, and airemlf90: under test | + | |
| - | | + | **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 36: | Line 34: | ||
| * 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) | ||
| - | | + | * [[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 | + | **No longer updated (as of May 2022)** |
| - | * [[readme.pregsf90|PREGSF90]] – genomic | + | * [[readme.blupf90|BLUPF90]] - BLUP in memory |
| - | * [[readme.pregsf90|POSTGSF90]] – genomic | + | * [[readme.reml|REMLF90]] - accelerated EM REML |
| + | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) | ||
| + | * [[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.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects | ||
| + | * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances | ||
| + | * 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.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits | ||
| + | * CBLUP90 | ||
| + | * CBLUP90THR - as above but with thresholds computed and many linear traits | ||
| + | * 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 | ||
| + | * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations | ||
| Other programming contributions were made by Miguel Perez-Enciso '' | Other programming contributions were made by Miguel Perez-Enciso '' | ||
application_programs.txt · Last modified: 2024/04/17 19:03 by andres