Differences

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--- application_programs [2022/05/06 18:01] – dani
+++ application_programs [2022/05/10 20:59] – dani
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 Download {{:blupf90_all7.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. ''inbupgf90'')
+\\
+**Main programs**
   * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90
   * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
-  * [[readme.gibbsf90new|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
-  * CBLUP90  - solutions for bivariate linear-threshold models (works only for 2 trait model: threshold and linear)
-  * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray)
-  * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic
-  * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic
-  * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic
   * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
   * [[Readme.Renumf90|RENUMF90]] - a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets
-  * [[Readme.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar)
+  * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar)
-  * [[Readme.SeekParentf90|SEEKPARENTF90]] -  a program to verify paternity and parent discovery using SNP markers (I. Aguilar)
+  * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar)
   * [[Readme.pedictf90|PREDICTF90]] - a program to calculate adjusted y, y_hat, and residuals (I. Aguilar)
-  * PREDF90 - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution
+  * [[Readme.predf90|PREDF90]] - a program to predict direct genomic value (DGV) for animals based on genotypes and SNP solution
   * [[readme.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information (Y. Masuda)
+  * [[Readme.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar)
+  * [[Readme.SeekParentf90|SEEKPARENTF90]] -  a program to verify paternity and parent discovery using SNP markers (I. Aguilar)
+/*Included in application programs*/
 Available by request
@@ Line 40: / Line 40: @@
   * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, and BLUP90IOD2HR: under test
-Included in application programs
+Deprecated programs (as of May 2022)
-  * [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar)
-  * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar)
-Deprecated programs
   * [[readme.blupf90|BLUPF90]] - BLUP in memory
   * [[readme.reml|REMLF90]] - accelerated EM REML
@@ Line 55: / Line 51: @@
   * [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified with several options (S. Tsuruta)
   * [[readme.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits
+  * CBLUP90  - solutions for bivariate linear-threshold models (works only for 2 trait model: threshold and linear)
+  * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray)
+  * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic
+  * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic
+  * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic
 Other programming contributions were made by Miguel Perez-Enciso ''(user_file)'' and François Guillaume (Jenkins hashing functions).