Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision |
faq [2012/05/16 14:18] – shogo | faq [2018/08/21 20:01] – [REML] shogo |
---|
====== FAQ for BLUPF90 programs ====== | ====== FAQ: examples and options for BLUPF90 family programs ====== |
| |
==== Input files ==== | Download {{:blupf90_ALL6.pdf|BLUPF90 manual}} |
| |
| ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ==== |
| |
* [[http://nce.ads.uga.edu/html/projects/FAQ_data.html|data]] | * [[[[FAQ.data|data]] |
* [[http://nce.ads.uga.edu/html/projects/FAQ_pedigree.html|pedigree]] | * [[[[FAQ.pedigree|pedigree]] |
| * [[[[FAQ.parameter|parameter]] |
| * [[[[FAQ.example|examples]] |
| |
==== Data preparation program ==== | ==== Data preparation program ==== |
| |
* [[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]] | * [[[[FAQ.renum_example|examples]] |
| |
==== Frequent mistakes in a parameter file for BLUPF90 programs ==== | ==== REML ==== |
| |
* [[http://nce.ads.uga.edu/html/projects/FAQ_param.html|parameter files for various models]] | * [[readme.reml|remlf90]]: EM algorithm |
* [[http://nce.ads.uga.edu/html/projects/FAQ_parameter.html|examples]] | * [[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)]] |
| * [[readme.blupf90|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90 |
| |
=== REML === | ==== 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 (known) variances |
| |
* [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|remlf90 (ver 1.76)]]: EM algorithm | * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits |
* [[http://nce.ads.uga.edu/html/projects/FAQ_reml.html|airemlf90 (ver 1.99)]]: Average Information REML + REMLF90 - Standard Errors (PDF) | * [[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.gibbs|gibbsf90test]]: This is a beta version for a combined Gibbs program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 |
| |
=== Gibbs sampling === | ==== Post-Gibbs Analysis ==== |
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 | * [[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. |
* gibbs2f90 (ver 1.76) read me | ==== BLUP ==== |
* gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances | |
* thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model | |
| |
=== Post-Gibbs Analysis === | * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG |
| * [[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, ... |
| ==== Accuracy (approximation) ==== |
| |
postgibbsf90 (ver 3.02) read me: Needs Gibbs samples and gnuplot (use postgibbsold for old Gibbs sampler programs) | * [[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) |
| |
=== BLUP === | ==== Genomic Analysis ==== |
| |
blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF | * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS) |
blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions) | * [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS) |
cblup90iod2 (ver 3.16) read me: Threshold model + linear model for a large number of equations (available only under some conditions) | * [[readme.predf90|predf90]]: Prediction of EBV using only SNP |
| |
Accuracy | ==== Technical problems in Windows / Linux ==== |
| |
accf90 : (ver 1.63) read me: Accuracy (reliability) for a large number of animals (available only under some conditions) | * [[FAQ.windows|System Error]]: Received a message like "The program can't start because libiomp5md.dll is missing..." in Windows. |
| * [[FAQ.segfault|Segmentation Fault]]: Received a message with "Segmentation fault" |
Genomic Analysis | * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program? |
| |
preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs | |