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--- faq [2023/12/20 23:25] – [Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs] shogo
+++ faq [2023/12/28 22:39] – [Frequent mistakes in data, pedigree, and parameter files for BLUPF90 programs] shogo
@@ Line 1: / Line 1: @@
-======  FAQ: examples and options for BLUPF90 family programs ======
+======  FAQ: examples, options, and tips for BLUPF90 family programs ======
 Download {{:blupf90_ALL8.pdf|BLUPF90 manual}}
@@ Line 26: / Line 26: @@
     * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90
     * [[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)]]
     * [[FAQ.vc#I got weird messages and nonsense estimates in AI REML. What is it?|I got weird messages and nonsense estimates in AI REML. What is it?]]
-=== Gibbs sampler ===
+=== 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
     * [[readme.gibbsf90plus|gibbsf90+]]: This is a combination of Gibbs programs: gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
     * [[readme.gibbs1|gibbs1f90]]: Faster than GIBBS2F90 without missing traits
     * [[readme.gibbs2|gibbs2f90]]: Useful with missing traits
@@ Line 39: / Line 41: @@
     * [[readme.thrgibbs1|thrgibbs1f90]]: Threshold + linear model
     * [[readme.thrgibbs3|thrgibbs3f90]]: Threshold + linear model with heterogeneous residual variances
     * [[faq.gibbs|General questions]]: Common to all Gibbs samplers
@@ Line 48: / Line 51: @@
     * [[readme.blupf90plus|blupf90+]]: This is a combination of remlf90, airemlf90, and blupf90
-    * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iodrr, blup90iod2hr, and blup90mbe with new features
+    * [[readme.pcgtest|blup90iod3 (new blup90iod)]] - a combined program of blup90iod2, blu90iod2r, blup90iod2hr, and blup90mbe2 with new features
     * [[readme.thr1pcg|cblup90iod2]]: (G)BLUP with threshold + linear model for a large number of equations (available only under some conditions)
     * [[readme.predictf90|predictf90]]: Calculates y-hat
@@ Line 69: / Line 72: @@
     * [[readme.pregsf90|postGSf90]]: Post-analysis of genomic programs with options (GWAS)
     * [[readme.predf90|predf90]]: Prediction of EBV using only SNP
+    * [[readme.qcf90|qcf90]] - a quality-control tool on genotypes and pedigree information
+=== Additional programs ===
+    * [[Readme.Inbupgf90|inbupgf90]] - a program to calculate inbreeding coefficients with incomplete pedigree
+    * [[Readme.SeekParentf90|seekparentf90]] -  a program to verify paternity and parent discovery using SNP markers