faq
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faq [2012/05/28 13:33] – shogo | faq [2019/03/28 19:48] – [FAQ: examples and options for BLUPF90 family programs] yutaka | ||
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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? | ||
- | ==== Data preparation program | + | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs |
- | * [[http:// | + | * [[[[FAQ.data|data]] |
- | * [[http://nce.ads.uga.edu/ | + | * [[[[FAQ.pedigree|pedigree]] |
+ | * [[[[FAQ.parameter|parameter]] | ||
+ | * [[[[FAQ.example|examples]] | ||
- | ==== Frequent mistakes in a parameter file for BLUPF90 programs | + | ==== Data preparation program |
- | * [[http://nce.ads.uga.edu/ | + | * [[[[readme.renumf90|renumf90]] |
- | * [[http:// | + | * [[[[FAQ.renum_example|examples]] |
==== REML ==== | ==== REML ==== | ||
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.reml|remlf90]]: EM algorithm |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.aireml|airemlf90]]: |
+ | * [[readme.blupf90new|blupf90test]]: | ||
- | ==== Gibbs sampling | + | ==== 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 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) |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.gibbs1|gibbs1f90]]: |
- | * [[http:// | + | * [[readme.gibbs2|gibbs2f90]]: Useful with missing traits |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.gibbs3|gibbs3f90]]: |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.thrgibbs1|thrgibbs1f90]]: |
+ | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
+ | * [[readme.gibbsf90new|gibbsf90test]]: | ||
==== Post-Gibbs Analysis ==== | ==== Post-Gibbs Analysis ==== | ||
- | * [[http:// | + | * [[readme.postgibbs|postgibbsf90]]: |
==== BLUP ==== | ==== BLUP ==== | ||
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.blupf90|blupf90]]: |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.predictf90|predictf90]]: Calculates y-hat |
- | * [[http://nce.ads.uga.edu/ | + | * [[readme.pcg2|blup90iod2]]: (G)BLUP for a large number of equations (available only under some conditions) |
+ | * [[readme.pcg2r|blup90iod2r]]: (G)BLUP with GIBBS3F90-type heterogeneous residual variance for a large number of equations (available only under some conditions) | ||
+ | * [[readme.pcg2hr|blup90iod2hr]]: | ||
+ | * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold | ||
+ | * [[blup90mbe2]]: | ||
+ | ==== Accuracy (approximation) ==== | ||
- | ==== Accuracy ==== | ||
- | |||
- | * [[http:// | ||
* [[readme.acc|accf90]]: | * [[readme.acc|accf90]]: | ||
+ | * [[readme.accgs|accf90GS]]: | ||
==== Genomic Analysis ==== | ==== Genomic Analysis ==== | ||
- | * [[readme.pregsf90|PreGSF90]]: Pre-analysis of genomic programs | + | * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs |
+ | * [[readme.pregsf90|postGSf90]]: | ||
+ | * [[readme.predf90|predf90]]: | ||
faq.txt · Last modified: 2024/05/17 18:17 by dani