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faq [2012/05/15 07:41] – andres | faq [2012/05/28 14:31] – ignacio |
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* data | * [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] |
* pedigree | * [[http://nce.ads.uga.edu/html/projects/FAQ_pedigree.html|pedigree]] |
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==== Data preparation program ==== | ==== Data preparation program ==== |
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renumf90 (ver 1.92) read me | * [[[[readme.renumf90|renumf90]] |
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 ==== | ==== Frequent mistakes in a parameter file for BLUPF90 programs ==== |
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parameter files for various models | * [[http://nce.ads.uga.edu/html/projects/FAQ_param.html|parameter files for various models]] |
examples | * [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] |
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REML | ==== REML ==== |
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remlf90 (ver 1.76) read me: EM algorithm - PDF | * [[readme.reml|remlf90]]: EM algorithm |
airemlf90 (ver 1.99) read me: Average Information REML + REMLF90 - Standard Errors (PDF) | * [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|remlf90 (ver 1.76)]] |
| * [[readme.aireml|airemlf90]]: Average Information REML + REMLF90 |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_aireml.html|airemlf90 (ver 1.101)]] - [[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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gibbs1f90 (ver 1.42) read me: Faster than GIBBS2F90 without missing traits | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits |
gibbs2f90 (ver 1.76) read me | * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs1.html|gibbs1f90 (ver 1.43)]] |
gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances | * [[readme.gibbs2|gibbs2f90]]: |
thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs2.html|gibbs2f90 (ver 1.81)]] |
| * [[readme.gibbs3|gibbs3f90]]: Heterogeneous residual variances |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs3.html|gibbs3f90 (ver 1.79)]] |
| * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold model + linear model |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_thrgibbs1.html|thrgibbs1f90(b) (ver 2.102)]] |
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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) |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_postgibbs.html|postgibbsf90 (ver 3.04)]] |
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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 |
blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | * [[http://nce.ads.uga.edu/html/projects/FAQ_blup.html|blupf90 (ver 1.45)]] |
cblup90iod2 (ver 3.16) read me: Threshold model + linear model 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) |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_pcg2.html|blup90iod2 (ver 3.81)]] |
| * [[readme.thr1pcg|cblup90iod]]: BLUP with threshold model + linear model 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)]] |
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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) |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_acc.html|accf90 (ver 1.66)]] |
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Genomic Analysis | ==== Genomic Analysis ==== |
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| * [[readme.pregsf90|PreGSF90]]: Pre-analysis of genomic programs |
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preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs | |