faq
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
faq [2012/07/13 11:52] – shogo | faq [2024/01/09 02:54] – [Modelling] shogo | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== | + | ====== |
- | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ==== | + | Download {{: |
+ | |||
+ | ==== Technical problems and segmentation fault ==== | ||
+ | |||
+ | * [[FAQ.segfault|Segmentation Fault]]: Received a message with " | ||
+ | * [[FAQ.windows|System Error]]: Received a message like "The program can't start because libiomp5md.dll is missing..." | ||
+ | * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program? | ||
+ | * [[FAQ.intellibs|Installation of Intel Libraries]]: | ||
+ | |||
+ | |||
+ | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs | ||
* [[[[FAQ.data|data]] | * [[[[FAQ.data|data]] | ||
Line 8: | Line 18: | ||
* [[[[FAQ.example|examples]] | * [[[[FAQ.example|examples]] | ||
- | ==== Data preparation program | + | === Data preparation program === |
* [[[[readme.renumf90|renumf90]] | * [[[[readme.renumf90|renumf90]] | ||
* [[[[FAQ.renum_example|examples]] | * [[[[FAQ.renum_example|examples]] | ||
- | ==== REML ==== | + | === REML === |
- | * [[readme.reml|remlf90]]: EM algorithm | + | * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 |
+ | |||
+ | * [[readme.reml|remlf90]]: EM algorithm | ||
* [[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?]] | ||
- | ==== 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.gibbs1|gibbs1f90]]: | * [[readme.gibbs1|gibbs1f90]]: | ||
* [[readme.gibbs2|gibbs2f90]]: | * [[readme.gibbs2|gibbs2f90]]: | ||
- | * [[readme.gibbs3|gibbs3f90]]: | + | * [[readme.gibbs3|gibbs3f90]]: |
* [[readme.thrgibbs1|thrgibbs1f90]]: | * [[readme.thrgibbs1|thrgibbs1f90]]: | ||
+ | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
- | ==== Post-Gibbs Analysis ==== | + | * [[faq.gibbs|General questions]]: |
- | * [[readme.postgibbs|postgibbsf90]]: | + | === Post-Gibbs |
- | ==== BLUP ==== | + | * [[readme.postgibbs|postgibbsf90]]: |
- | * [[readme.blupf90|blupf90]]: | + | === BLUP === |
- | * [[readme.pcg2|blup90iod2]]: | + | |
- | * [[readme.thr1pcg|cblup90iod]]: | + | |
- | ==== Accuracy | + | * [[readme.blupf90plus|blupf90+]]: |
+ | * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iod2r, blup90iod2hr, | ||
+ | * [[readme.thr1pcg|cblup90iod2]]: | ||
+ | * [[readme.predictf90|predictf90]]: | ||
+ | |||
+ | * [[readme.blupf90|blupf90]]: | ||
+ | * [[readme.pcg2|blup90iod2]]: | ||
+ | * [[readme.pcg2r|blup90iod2r]]: | ||
+ | * [[readme.pcg2hr|blup90iod2hr]]: | ||
+ | * [[blup90mbe2]]: | ||
+ | |||
+ | === Accuracy | ||
* [[readme.acc|accf90]]: | * [[readme.acc|accf90]]: | ||
+ | * [[readme.accgs|accf90GS]]: | ||
+ | * [[readme.accgs2|accf90GS2]]: | ||
- | ==== Genomic Analysis | + | === Genomic Analysis === |
* [[readme.pregsf90|preGSf90]]: | * [[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 ==== | ||
+ | * 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