faq
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faq [2023/12/20 23:31] – [Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs] shogo | faq [2024/01/09 03:24] – [Modeling] shogo | ||
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- | ====== | + | ====== |
Download {{: | Download {{: | ||
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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 | + | * [[readme.qcf90|qcf90]] - a quality-control tool on genotypes and pedigree information |
=== Additional programs === | === Additional programs === | ||
- | * [[Readme.Inbupgf90|inbupgf90]] - a program to calculate inbreeding coefficients with incomplete pedigree | + | * [[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 (I. Aguilar) | + | * [[Readme.SeekParentf90|seekparentf90]] - a program to verify paternity and parent discovery using SNP markers |
+ | |||
+ | |||
+ | ===== Modeling ===== | ||
+ | < | ||
+ | |||
+ | * Sire model (cg: contemporary group) | ||
+ | y = μ + cg + ... + sire + e | ||
+ | y = μ + cg + ... + sire + MGS + e | ||
+ | where cg = common environment: | ||
+ | * Animal model (pe: permanent environment) | ||
+ | * Single record / animal | ||
+ | y = μ + cg + ... + animal + e | ||
+ | * Multiple records / animal | ||
+ | y = μ + cg + ... + animal + pe + e | ||
+ | * Random regressions f(t) | ||
+ | y = μ + cg + ... + f(t1) + f(t2)*animal + f(t3)*pe + e | ||
+ | where f(t) = a function of t (t: continuous variable) | ||
+ | * Maternal effect model (mpe: maternal permanent environment) | ||
+ | y = μ + cg + ... + animal + maternal + mpe + e | ||
+ | |||
+ | </ | ||
faq.txt · Last modified: 2024/05/17 18:17 by dani