Differences

This shows you the differences between two versions of the page.

--- faq [2012/05/16 14:20] – shogo
+++ faq [2018/08/21 19:59] – [Gibbs sampler] shogo
@@ Line 1: / Line 1: @@
-======  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 ====
-   * [[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)]]
-=== 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 - [[http://nce.ads.uga.edu/html/projects/AI_SE.pdf|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 programs 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