faq
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faq [2012/05/16 14:16] – shogo | faq [2024/01/09 03:06] – [Modelling] shogo | ||
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- | ====== | + | ====== |
- | ==== Input files ==== | + | Download {{: |
+ | ==== Technical problems and segmentation fault ==== | ||
- | | + | |
- | * [[http://nce.ads.uga.edu/ | + | * [[FAQ.windows|System Error]]: Received a message like "The program can't start because libiomp5md.dll is missing..." in Windows. |
+ | * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program? | ||
+ | * [[FAQ.intellibs|Installation of Intel Libraries]]: | ||
- | ==== Data preparation program ==== | ||
- | * [[http:// | + | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ===== |
- | * [[http:// | + | |
- | ==== Frequent mistakes in a parameter | + | * [[[[FAQ.data|data]] |
+ | * [[[[FAQ.pedigree|pedigree]] | ||
+ | * [[[[FAQ.parameter|parameter]] | ||
+ | * [[[[FAQ.example|examples]] | ||
- | * [[http://nce.ads.uga.edu/ | + | === Data preparation program === |
- | | + | |
+ | * [[[[readme.renumf90|renumf90]] | ||
+ | * [[[[FAQ.renum_example|examples]] | ||
=== REML === | === REML === | ||
- | * remlf90 (ver 1.76) read me: EM algorithm - PDF | + | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, |
- | * airemlf90 | + | |
- | === Gibbs sampling === | + | * [[readme.reml|remlf90]]: |
- | OPTIONs for priors | + | * [[readme.aireml|airemlf90]]: |
+ | * [[FAQ.vc#I got weird messages | ||
- | * gibbs1f90 | + | === Gibbs Sampler === |
- | * gibbs2f90 (ver 1.76) read me | + | 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 |
- | * gibbs3f90 | + | |
- | * thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | + | * [[readme.gibbsf90plus|gibbsf90+]]: |
+ | |||
+ | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits | ||
+ | * [[readme.gibbs2|gibbs2f90]]: | ||
+ | * [[readme.gibbs3|gibbs3f90]]: With heterogeneous | ||
+ | * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold | ||
+ | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
+ | |||
+ | * [[faq.gibbs|General questions]]: | ||
=== Post-Gibbs Analysis === | === Post-Gibbs Analysis === | ||
- | | + | |
=== BLUP === | === BLUP === | ||
- | blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | + | |
- | blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | + | * [[readme.pcgtest|blup90iod3 |
- | | + | * [[readme.thr1pcg|cblup90iod2]]: |
+ | * [[readme.predictf90|predictf90]]: Calculates y-hat | ||
+ | |||
+ | * [[readme.blupf90|blupf90]]: | ||
+ | | ||
+ | * [[readme.pcg2r|blup90iod2r]]: | ||
+ | * [[readme.pcg2hr|blup90iod2hr]]: (G)BLUP with AIREMLF90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | ||
+ | | ||
+ | |||
+ | === Accuracy (approximation) === | ||
+ | |||
+ | * [[readme.acc|accf90]]: Accuracy (reliability) | ||
+ | * [[readme.accgs|accf90GS]]: | ||
+ | * [[readme.accgs2|accf90GS2]]: | ||
+ | |||
+ | === Genomic Analysis === | ||
+ | |||
+ | * [[readme.pregsf90|preGSf90]]: | ||
+ | * [[readme.pregsf90|postGSf90]]: | ||
+ | * [[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 ===== | ||
+ | < | ||
- | Accuracy | + | * Sire model |
+ | y = μ + ... + sire + e | ||
+ | y = μ + ... + sire + MGS + e | ||
+ | * Animal model (pe: permanent environment) | ||
+ | * Single record / animal | ||
+ | y = μ + ... + animal + e | ||
+ | * Multiple records / animal | ||
+ | y = μ + ... + animal + pe + e | ||
+ | * Random regressions f(t) | ||
+ | y = μ + ... + 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 + ... + animal + maternal + mpe + e | ||
- | accf90 : (ver 1.63) read me: Accuracy (reliability) for a large number of animals (available only under some conditions) | + | </ |
- | Genomic Analysis | ||
- | preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs |
faq.txt · Last modified: 2024/05/17 18:17 by dani