faq
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faq [2012/05/10 19:48] – created ignacy | faq [2023/09/04 20:34] – [Individual program] shogo | ||
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- | FAQ for BLUPF90 programs | + | ====== |
- | Input files | + | |
- | data | + | Download {{: |
- | pedigree | + | |
- | Data preparation program | + | ==== Technical problems and segmentation fault ==== |
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- | | + | |
+ | * [[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 a parameter file for BLUPF90 programs | + | ==== Variance Components ==== |
- | | + | |
- | examples | + | |
- | REML | + | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ===== |
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- | | + | |
+ | * [[[[FAQ.parameter|parameter]] | ||
+ | * [[[[FAQ.example|examples]] | ||
- | Gibbs sampling | + | ==== Individual program ==== |
- | OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed variances | + | |
- | gibbs1f90 (ver 1.42) read me: Faster than GIBBS2F90 without missing traits | + | === Data preparation program === |
- | gibbs2f90 (ver 1.76) read me | + | |
- | gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances | + | |
- | thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | + | |
- | Post-Gibbs Analysis | + | * [[[[readme.renumf90|renumf90]] |
+ | * [[[[FAQ.renum_example|examples]] | ||
- | postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs) | + | === REML === |
- | BLUP | + | * [[readme.reml|remlf90]]: |
+ | * [[readme.aireml|airemlf90]]: | ||
+ | * [[readme.blupf90plus|blupf90+]]: | ||
- | blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | + | === Gibbs sampler === |
- | | + | OPTIONs for priors and degrees |
- | cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations | + | |
- | Accuracy | + | * [[readme.gibbs1|gibbs1f90]]: |
+ | * [[readme.gibbs2|gibbs2f90]]: | ||
+ | * [[readme.gibbs3|gibbs3f90]]: | ||
+ | * [[readme.thrgibbs1|thrgibbs1f90]]: | ||
+ | * [[readme.thrgibbs3|thrgibbs3f90]]: | ||
+ | * [[readme.gibbsf90plus|gibbsf90+]]: | ||
+ | * [[faq.gibbs|General questions]]: | ||
- | accf90 | + | === Post-Gibbs Analysis === |
+ | |||
+ | * [[readme.postgibbs|postgibbsf90]]: Statistics and graphics for convergence diagnosis and post-Gibbs analysis | ||
+ | |||
+ | === BLUP === | ||
+ | |||
+ | * [[readme.blupf90|blupf90]]: | ||
+ | * [[readme.blupf90plus|blupf90+]]: | ||
+ | * [[readme.predictf90|predictf90]]: | ||
+ | * [[readme.pcg2|blup90iod2]]: | ||
+ | * [[readme.pcg2r|blup90iod2r]]: | ||
+ | * [[readme.pcg2hr|blup90iod2hr]]: | ||
+ | * [[readme.thr1pcg|cblup90iod2]]: | ||
+ | * [[blup90mbe2]]: | ||
+ | * [[readme.pcgtest|BLUP90IOD3 (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, | ||
+ | |||
+ | === 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]]: | ||
- | Genomic Analysis | ||
- | preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs |
faq.txt · Last modified: 2024/05/17 18:17 by dani