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faq [2012/05/16 14:26] – shogo | faq [2012/05/29 17:26] – shogo |
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====== FAQ for BLUPF90 programs ====== | ====== FAQ for BLUPF90 programs ====== |
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==== Input files ==== | ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ==== |
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| * [[[[FAQ.data|data]] |
* [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] | * [[[[FAQ.pedigree|pedigree]] |
* [[http://nce.ads.uga.edu/html/projects/FAQ_pedigree.html|pedigree]] | * [[[[FAQ.parameter|parameter]] |
| * [[[[FAQ.example|examples]] |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] |
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==== Data preparation program ==== | ==== Data preparation program ==== |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_renum.html|renumf90 (ver 1.92)]] | * [[[[readme.renumf90|renumf90]] |
* [[http://nce.ads.uga.edu/html/projects/FAQ_para_renum.html|examples]] | * [[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 ==== | |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_param.html|parameter files for various models]] | |
* [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] | |
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==== REML ==== | ==== REML ==== |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|remlf90 (ver 1.76)]]: EM algorithm | * [[readme.reml|remlf90]]: EM algorithm [[http://nce.ads.uga.edu/html/projects/remlf90.pdf|REMLF90 (PDF)]] |
* [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|airemlf90 (ver 1.99)]]: Average Information REML + REMLF90 - [[http://nce.ads.uga.edu/html/projects/AI_SE.pdf|Standard Errors (PDF)]] | * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 [[http://nce.ads.uga.edu/html/projects/AI_SE.pdf|Standard Errors (PDF)]] |
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==== 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 variances |
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* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs1.html|gibbs1f90 (ver 1.42)]]: Faster than GIBBS2F90 without missing traits | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits |
* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs2.html|gibbs2f90 (ver 1.76)]] | * [[readme.gibbs2|gibbs2f90]]: |
* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs3.html|gibbs3f90 (ver 1.77)]]: Heterogeneous residual variances | * [[readme.gibbs3|gibbs3f90]]: Heterogeneous residual variances |
* [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs1.html|thrgibbs1f90(b) (ver 2.100)]]: Threshold model + linear model | * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold model + linear model |
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==== Post-Gibbs Analysis ==== | ==== Post-Gibbs Analysis ==== |
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postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs) | * [[readme.postgibbs|postgibbsf90]]: Statistics and graphics for post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs) |
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==== BLUP ==== | ==== BLUP ==== |
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blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | * [[readme.blupf90|blupf90]]: BLUP with SOR, FSPAK or PCG [[http://nce.ads.uga.edu/html/projects/blupf90.pdf|BLUPF90 (PDF)]] |
blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | * [[readme.pcg2|blup90iod2]]: BLUP 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) | * [[readme.thr1pcg|cblup90iod]]: BLUP with threshold model + linear model for a large number of equations (available only under some conditions) |
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==== Accuracy ==== | ==== Accuracy ==== |
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accf90 : (ver 1.63) read me: 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) |
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==== Genomic Analysis ==== | ==== Genomic Analysis ==== |
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preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs | * [[readme.pregsf90|PreGSF90]]: Pre-analysis of genomic programs |