faq
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faq [2012/05/16 14:26] – shogo | faq [2024/01/09 02:57] – [Modelling] shogo | ||
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- | ====== | + | ====== |
- | ==== Input files ==== | + | Download {{: |
+ | ==== Technical problems and segmentation fault ==== | ||
- | * [[http:// | + | * [[FAQ.segfault|Segmentation Fault]]: Received a message with " |
- | * [[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:// | + | === Data preparation program === |
- | * [[http:// | + | |
- | ==== REML ==== | + | * [[[[readme.renumf90|renumf90]] |
+ | * [[[[FAQ.renum_example|examples]] | ||
- | * [[http:// | + | === REML === |
- | * [[http:// | + | |
- | ==== Gibbs sampling ==== | + | * [[readme.blupf90plus|blupf90+]]: |
- | OPTIONs for priors and degrees | + | |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.reml|remlf90]]: EM algorithm |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances |
- | * [[http:// | + | * [[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?]] |
- | * [[http://nce.ads.uga.edu/ | + | |
- | ==== Post-Gibbs Analysis ==== | + | === 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 | ||
- | | + | |
- | ==== BLUP ==== | + | * [[readme.gibbs1|gibbs1f90]]: |
+ | * [[readme.gibbs2|gibbs2f90]]: | ||
+ | * [[readme.gibbs3|gibbs3f90]]: | ||
+ | * [[readme.thrgibbs1|thrgibbs1f90]]: | ||
+ | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
- | | + | |
- | blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | + | |
- | cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations (available only under some conditions) | + | |
- | ==== Accuracy ==== | + | === Post-Gibbs Analysis |
- | | + | |
+ | |||
+ | === BLUP === | ||
+ | |||
+ | * [[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 (approximation) === | ||
+ | |||
+ | * [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | ||
+ | * [[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 ===== | ||
+ | < | ||
+ | * 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 | ||
+ | </ | ||
- | ==== Genomic Analysis ==== | ||
- | preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs |
faq.txt · Last modified: 2024/05/17 18:17 by dani