Differences

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

--- faq [2018/07/09 19:21] – [Genomic Analysis] shogo
+++ faq [2019/12/13 07:45] – [Gibbs sampler] yutaka
@@ Line 1: / Line 1: @@
 ======  FAQ: examples and options for BLUPF90 family programs ======
-Download {{:blupf90_ALL6.pdf|BLUPF90 manual}}
+Download {{:blupf90_ALL7.pdf|BLUPF90 manual}}
+==== Technical problems and segmentation fault ====
+    * [[FAQ.segfault|Segmentation Fault]]: Received a message with "Segmentation fault"
+    * [[FAQ.windows|System Error]]: Received a message like "The program can't start because libiomp5md.dll is missing..." in Windows.
+    * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program?
+    * [[FAQ.intellibs|Installation of Intel Libraries]]: For users with customized programs
 ==== Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs ====
@@ Line 19: / Line 26: @@
     * [[readme.reml|remlf90]]: EM algorithm
     * [[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.blupf90new|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90
 ==== Gibbs sampler ====
@@ Line 28: / Line 36: @@
     * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model
     * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances
+    * [[readme.gibbsf90new|gibbsf90test]]: This is a beta version for a combined Gibbs program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
+    * [[faq.gibbs|General questions]]: Common to all Gibbs samplers
 ==== Post-Gibbs Analysis ====
@@ Line 35: / Line 45: @@
     * [[readme.blupf90|blupf90]]: (G)BLUP with SOR, FSPAK or PCG
+    * [[readme.blupf90new|blupf90test]]: This is a beta version for a combined program of airemlf90 and blupf90
+    * [[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)
@@ Line 40: / Line 52: @@
     * [[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) ====
     * [[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)
+    * [[readme.accgs|accf90GS]]: Accuracy (reliability) for a large number of animals with genotypes (available only under some conditions); requires options
 ==== Genomic Analysis ====
@@ Line 50: / Line 61: @@
     * [[readme.pregsf90|preGSf90]]: Pre-analysis of genomic programs with options, including options for postGSf90 (GWAS)
     * [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS)
-    * [[readme.predf90|predf90]]: Predict EBV with only SNP
+    * [[readme.predf90|predf90]]: Prediction of EBV using only SNP
-==== Technical problems in Windows / Linux ====
-    * [[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"
-    * [[FAQ.openmp|Better settings for OpenMP]]: How should I define the number of threads used with a program?