application_programs
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| application_programs [2022/05/04 00:35] – dani | application_programs [2022/05/06 18:15] – 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.blupf90|BLUPF90]] - BLUP in memory | + | |
| - | | + | * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, |
| - | * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML | + | |
| * CBLUP90 | * CBLUP90 | ||
| * 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 | ||
| - | * [[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 | ||
| * [[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 | ||
| * [[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.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) | ||
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| * 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 | ||
| * [[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.blupf90new|BLUPF90+ (new BLUPF90)]] - a combined program of blupf90, remlf90, and airemlf90 | + | |
| - | * [[readme.gibbsf90new|GIBBSF90+ (new GIBBSF90)]] - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, | + | |
| - | + | ||
| 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:// | ||
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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 | ||
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| * [[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 (new BLUP90IOD)]] - a combined program of BLUP90IOD2, | + | * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, |
| | | ||
| Included in application programs | Included in application programs | ||
| * [[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) | ||
| + | |||
| + | Deprecated programs (as of May 2022) | ||
| + | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
| + | * [[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 | ||
| 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