Differences

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--- faq [2012/05/10 19:48] – created ignacy
+++ faq [2014/11/20 12:10] – shogo
@@ Line 1: / Line 1: @@
-FAQ for BLUPF90 programs
+======  FAQ: examples and options for BLUPF90 family programs ======
-Input files
-    data
+Download {{:blupf90_all1.pdf|BLUPF90 manual}}
-    pedigree
-Data preparation program
+==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ====
-    renumf90 (ver 1.92) read me
+    * [[[[FAQ.data|data]]
-    examples
+    * [[[[FAQ.pedigree|pedigree]]
+    * [[[[FAQ.parameter|parameter]]
+    * [[[[FAQ.example|examples]]
-Frequent mistakes in a parameter file for BLUPF90 programs
+==== Data preparation program ====
-    parameter files for various models
+    * [[[[readme.renumf90|renumf90]]
-    examples
+    * [[[[FAQ.renum_example|examples]]
-REML
+==== REML ====
-    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)
+    * [[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)]]
-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 (known) variances
-    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
+    * [[readme.gibbs2|gibbs2f90]]: Useful with missing traits
-    gibbs3f90 (ver 1.77) read me: Heterogeneous residual variances
+    * [[readme.gibbs3|gibbs3f90]]: With heterogeneous residual variances
-    thrgibbs1f90(b) (ver 2.100) read me: Threshold model + linear model
+    * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model
+    * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances
-Post-Gibbs Analysis
+==== Post-Gibbs Analysis ====
-    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 convergence diagnosis and post-Gibbs analysis (use postgibbsold for old Gibbs sampler programs)
-BLUP
+==== BLUP ====
-    blupf90 (ver 1.45) read me: SOR, FSPAK or PCG - PDF
+    * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG
-    blup90iod2 (ver 3.78) read me: For a large number of equations (available only under some conditions)
+    * [[readme.pcg2|blup90iod2]]: (G)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|cblup90iod2]]: BLUP with threshold + linear model for a large number of equations (available only under some conditions)
-Accuracy
+==== Accuracy ====
-    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)
+    * [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions)
-Genomic Analysis
+==== Genomic Analysis ====
+    * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS)
-    preGSf90 (ver 1.6) read me: Pre-analysis of genomic programs