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faq [2018/07/09 19:21] – [Genomic Analysis] shogo | faq [2019/02/22 01:21] – [Accuracy (approximation)] shogo |
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* [[readme.reml|remlf90]]: EM algorithm | * [[readme.reml|remlf90]]: EM algorithm |
* [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances [[http://nce.ads.uga.edu/html/projects/AI_SE_revised.pdf|Standard Errors (PDF)]] | * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances [[http://nce.ads.uga.edu/html/projects/AI_SE_revised.pdf|Standard Errors (PDF)]] |
| * [[readme.blupf90new|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90 |
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==== Gibbs sampler ==== | ==== Gibbs sampler ==== |
* [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model | * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model |
* [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances | * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances |
| * [[readme.gibbsf90new|gibbsf90test]]: This is a beta version for a combined Gibbs program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 |
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==== Post-Gibbs Analysis ==== | ==== Post-Gibbs Analysis ==== |
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* [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG | * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG |
| * [[readme.predictf90|predictf90]]: Calculates y-hat |
* [[readme.pcg2|blup90iod2]]: (G)BLUP for a large number of equations (available only under some conditions) | * [[readme.pcg2|blup90iod2]]: (G)BLUP for a large number of equations (available only under some conditions) |
* [[readme.pcg2r|blup90iod2r]]: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | * [[readme.pcg2r|blup90iod2r]]: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions) |
* [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions) | * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions) |
* [[blup90mbe2]]: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, ... | * [[blup90mbe2]]: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, ... |
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==== Accuracy (approximation) ==== | ==== Accuracy (approximation) ==== |
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* [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | * [[readme.acc|accf90]]: Calculates accuracy (reliability) for a large number of animals (available only under some conditions) |
* [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions) | * [[readme.accgs|accf90GS]]: Calculates accuracy (reliability) for a large number of animals with genotypes (available only under some conditions) |
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==== Genomic Analysis ==== | ==== Genomic Analysis ==== |