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faq [2012/05/28 13:33] – shogo | faq [2023/12/20 23:22] – [Individual program] shogo |
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====== FAQ for BLUPF90 programs ====== | ====== FAQ: examples and options for BLUPF90 family programs ====== |
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==== Input files ==== | Download {{:blupf90_ALL8.pdf|BLUPF90 manual}} |
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| ==== Technical problems and segmentation fault ==== |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] | * [[FAQ.segfault|Segmentation Fault]]: Received a message with "Segmentation fault" |
* [[http://nce.ads.uga.edu/html/projects/FAQ_pedigree.html|pedigree]] | * [[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]]: For users with customized programs |
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==== Data preparation program ==== | |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_renum.html|renumf90 (ver 1.98)]] | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ===== |
* [[http://nce.ads.uga.edu/html/projects/FAQ_para_renum.html|examples]] | |
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==== Frequent mistakes in a parameter file for BLUPF90 programs ==== | * [[[[FAQ.data|data]] |
| * [[[[FAQ.pedigree|pedigree]] |
| * [[[[FAQ.parameter|parameter]] |
| * [[[[FAQ.example|examples]] |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_param.html|parameter files for various models]] | === Data preparation program === |
* [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] | |
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==== REML ==== | * [[[[readme.renumf90|renumf90]] |
| * [[[[FAQ.renum_example|examples]] |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|remlf90 (ver 1.76)]]: EM algorithm | === REML === |
* [[http://nce.ads.uga.edu/html/projects/FAQ_aireml.html|airemlf90 (ver 1.101)]]: Average Information REML + REMLF90 - [[http://nce.ads.uga.edu/html/projects/AI_SE.pdf|Standard Errors (PDF)]] | |
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==== Gibbs sampling ==== | * [[readme.reml|remlf90]]: EM algorithm |
OPTIONs for priors and degrees of belief, for restarting from the last sampling, and for storing solutions and SD with or without fixed variances | * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 including heterogeneous residual variances [[http://nce.ads.uga.edu/html/projects/AI_SE_revised.pdf|Standard Errors (PDF)]] |
| * [[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?]] |
| * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs1.html|gibbs1f90 (ver 1.43)]]: Faster than GIBBS2F90 without missing traits | === Gibbs sampler === |
* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs2.html|gibbs2f90 (ver 1.81)]] | 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 |
* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs3.html|gibbs3f90 (ver 1.79)]]: Heterogeneous residual variances | |
* [[http://nce.ads.uga.edu/html/projects/FAQ_thrgibbs1.html|thrgibbs1f90(b) (ver 2.102)]]: Threshold model + linear model | |
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==== Post-Gibbs Analysis ==== | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits |
| * [[readme.gibbs2|gibbs2f90]]: Useful with missing traits |
| * [[readme.gibbs3|gibbs3f90]]: With heterogeneous residual variances |
| * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model |
| * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances |
| * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 |
| * [[faq.gibbs|General questions]]: Common to all Gibbs samplers |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_postgibbs.html|postgibbsf90 (ver 3.04)]]: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs) | === Post-Gibbs Analysis === |
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==== BLUP ==== | * [[readme.postgibbs|postgibbsf90]]: Statistics and graphics for convergence diagnosis and post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs). The graphs are created with gnuplot, which must be pre-installed. |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_blup.html|blupf90 (ver 1.45)]]: SOR, FSPAK or PCG - PDF | === BLUP === |
* [[http://nce.ads.uga.edu/html/projects/FAQ_pcg2.html|blup90iod2 (ver 3.81)]]: For a large number of equations (available only under some conditions) | |
* [[http://nce.ads.uga.edu/html/projects/FAQ_cblup90iod2.html|cblup90iod2 (ver 3.17)]]: Threshold model + linear model for a large number of equations (available only under some conditions) | |
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==== Accuracy ==== | * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG |
| * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90 |
| * [[readme.predictf90|predictf90]]: Calculates y-hat |
| * [[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]]: (G)BLUP with AIREMLF90-type heterogeneous residual variance for a large number of equations (available only under some conditions) |
| * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions) |
| * [[blup90mbe2]]: (G)BLUP for a large number of equations for multi-breed evaluations (available only under some conditions). The prior external EBV can be from other breeds, lines, foreign origins, ... |
| * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iodrr, blup90iod2hr, and blup90mbe with new features |
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| === Accuracy (approximation) === |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_acc.html|accf90 (ver 1.66)]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | |
* [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) | * [[readme.acc|accf90]]: Accuracy (reliability) for a large number of animals (available only under some conditions) |
| * [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options |
| * [[readme.accgs2|accf90GS2]]: New accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options |
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| === Genomic Analysis === |
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==== Genomic Analysis ==== | * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS) |
| * [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS) |
| * [[readme.predf90|predf90]]: Prediction of EBV using only SNP |
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* [[readme.pregsf90|PreGSF90]]: Pre-analysis of genomic programs | |
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