faq
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faq [2023/12/20 23:25] – [Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs] shogo | faq [2024/01/09 02:59] – [Modelling] shogo | ||
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- | ====== | + | ====== |
Download {{: | Download {{: | ||
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* [[readme.blupf90plus|blupf90+]]: | * [[readme.blupf90plus|blupf90+]]: | ||
+ | |||
* [[readme.reml|remlf90]]: | * [[readme.reml|remlf90]]: | ||
* [[readme.aireml|airemlf90]]: | * [[readme.aireml|airemlf90]]: | ||
* [[FAQ.vc#I got weird messages and nonsense estimates in AI REML. What is it?|I got weird messages and nonsense estimates in AI REML. What is it?]] | * [[FAQ.vc#I got weird messages and nonsense estimates in AI REML. What is it?|I got weird messages and nonsense estimates in AI REML. What is it?]] | ||
- | === Gibbs sampler | + | === Gibbs Sampler |
OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed (known) variances | OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed (known) variances | ||
* [[readme.gibbsf90plus|gibbsf90+]]: | * [[readme.gibbsf90plus|gibbsf90+]]: | ||
+ | |||
* [[readme.gibbs1|gibbs1f90]]: | * [[readme.gibbs1|gibbs1f90]]: | ||
* [[readme.gibbs2|gibbs2f90]]: | * [[readme.gibbs2|gibbs2f90]]: | ||
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* [[readme.thrgibbs1|thrgibbs1f90]]: | * [[readme.thrgibbs1|thrgibbs1f90]]: | ||
* [[readme.thrgibbs3|thrgibbs3f90]]: | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
+ | |||
* [[faq.gibbs|General questions]]: | * [[faq.gibbs|General questions]]: | ||
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* [[readme.blupf90plus|blupf90+]]: | * [[readme.blupf90plus|blupf90+]]: | ||
- | * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, | + | * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, |
* [[readme.thr1pcg|cblup90iod2]]: | * [[readme.thr1pcg|cblup90iod2]]: | ||
* [[readme.predictf90|predictf90]]: | * [[readme.predictf90|predictf90]]: | ||
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* [[readme.pregsf90|postGSf90]]: | * [[readme.pregsf90|postGSf90]]: | ||
* [[readme.predf90|predf90]]: | * [[readme.predf90|predf90]]: | ||
+ | * [[readme.qcf90|qcf90]] - a quality-control tool on genotypes and pedigree information | ||
+ | |||
+ | === Additional programs === | ||
+ | |||
+ | * [[Readme.Inbupgf90|inbupgf90]] - a program to calculate inbreeding coefficients with incomplete pedigree | ||
+ | * [[Readme.SeekParentf90|seekparentf90]] - a program to verify paternity and parent discovery using SNP markers | ||
+ | |||
+ | |||
+ | ===== Modelling ===== | ||
+ | < | ||
+ | |||
+ | * Sire model | ||
+ | y = μ + ... + sire + e | ||
+ | y = μ + ... + sire + MGS + e | ||
+ | * Animal model | ||
+ | * Single record / animal | ||
+ | y = μ + ... + animal + e | ||
+ | * Multiple records / animal | ||
+ | y = μ + ... + animal + pe + e | ||
+ | * Random regressions | ||
+ | y = μ + ... + f(t1) + f(t2)*animal + f(t3)*pe + e | ||
+ | * Maternal effect model | ||
+ | y = μ + ... + animal + mat + mpe + e | ||
+ | |||
+ | </ | ||
faq.txt · Last modified: 2024/05/17 18:17 by dani