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faq [2022/05/25 22:04] – [Individual program] dani | faq [2023/09/04 20:34] – [Individual program] 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 | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, 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|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 | * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 |
* [[faq.gibbs|General questions]]: Common to all Gibbs samplers | * [[faq.gibbs|General questions]]: Common to all Gibbs samplers |
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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.blupf90new|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 |
* [[readme.predictf90|predictf90]]: Calculates y-hat | * [[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.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, ... |
| * [[readme.pcgtest|BLUP90IOD3 (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, and BLUP90IOD2HR with new features |
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=== Accuracy (approximation) === | === Accuracy (approximation) === |
* [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | * [[readme.acc|accf90]]: 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); requires options | * [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options |
| * [[readme.accgs2|accf90GS2]]: New accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options |
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=== Genomic Analysis === | === Genomic Analysis === |