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 20:32] – dani | application_programs [2022/05/10 21:00] – dani | ||
|---|---|---|---|
| Line 5: | Line 5: | ||
| Download {{: | Download {{: | ||
| + | \\ | ||
| + | **Main programs** | ||
| * [[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, | ||
| * [[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.pedictf90|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*/ | /*Included in application programs*/ | ||
| - | * [[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) | ||
| - | 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 24: | Line 27: | ||
| * 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 a 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) | * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90) | ||
| Line 37: | Line 40: | ||
| * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, | * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, | ||
| | | ||
| - | Deprecated programs (as of May 2022) | + | **Deprecated programs (as of May 2022)** |
| * [[readme.blupf90|BLUPF90]] - BLUP in memory | * [[readme.blupf90|BLUPF90]] - BLUP in memory | ||
| * [[readme.reml|REMLF90]] - accelerated EM REML | * [[readme.reml|REMLF90]] - accelerated EM REML | ||
application_programs.txt · Last modified: 2024/06/19 14:22 by andres