| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision |
| faq [2012/05/16 14:20] – shogo | faq [2012/05/27 23:30] – ignacio |
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| * [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] | * [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_pedigree.html|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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| * [[http://nce.ads.uga.edu/html/projects/FAQ_renum.html|renumf90 (ver 1.92)]] | * [[http://nce.ads.uga.edu/html/projects/FAQ_renum.html|renumf90 (ver 1.98)]] |
| * [[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 ==== | ==== 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_param.html|parameter files for various models]] |
| * [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] | * [[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 | * [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|remlf90 (ver 1.76)]]: EM algorithm |
| * [[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)]] | * [[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 === | ==== Gibbs sampling ==== |
| 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 | * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs1.html|gibbs1f90 (ver 1.43)]]: Faster than GIBBS2F90 without missing traits |
| * gibbs2f90 (ver 1.76) read me | * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs2.html|gibbs2f90 (ver 1.81)]] |
| * gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances | * [[http://nce.ads.uga.edu/html/projects/FAQ_gibbs3.html|gibbs3f90 (ver 1.79)]]: Heterogeneous residual variances |
| * thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | * [[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 === | ==== 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) | * [[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) |
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| === BLUP === | ==== BLUP ==== |
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| blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | * [[http://nce.ads.uga.edu/html/projects/FAQ_blup.html|blupf90 (ver 1.45)]]: SOR, FSPAK or PCG - PDF |
| 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_pcg2.html|blup90iod2 (ver 3.81)]]: 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) | * [[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 | ==== Accuracy ==== |
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| accf90 : (ver 1.63) read me: 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)]]: 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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| | * [[readme.pregsf90|PreGSF90]]: Pre-analysis of genomic programs |
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| preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs | |
