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--- application_programs [2012/05/15 14:33] – andres
+++ application_programs [2018/06/20 20:49] – shogo
@@ Line 1: / Line 1: @@
-The programs support mixed models with multiple-correlated effects, multiple animal models and dominance.
+The [[distribution|programs]] support mixed models with multiple-correlated effects, multiple animal models and dominance.
-FIXME Should we link all programs to their Readme's and doc's? (AL)
+**Most** of the programs now support being called with the parameter file as an argument, e.g. <file> blupf90 renf90.par </file>. This avoids typing the name of the file in interactive or doing the trick <file> echo renf90.par | blupf90 </file>.
-   * BLUPF90 - BLUP in memory {{blupf90.pdf}}
+Download {{:blupf90_all7.pdf|BLUPF90 family manual}}. Note that some programs repertoried below are not in the manual (e.g. ''inbupgf90'')
-   *REMLF90 - accelerated EM REML {{remlf90.pdf}}
-   * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http://www.icrea.cat/Web/OtherSectionViewer.aspx?key=485&titol=Software:Qxpak | QxPak web page]]
+   * [[readme.blupf90|BLUPF90]] - BLUP in memory
-  * AIREMLF90 - Average Information REML (S. Tsuruta)
+   * [[readme.reml|REMLF90]] - accelerated EM REML
-  *  AIREMLRES - as above with support for heterogeneous residual variances (T. Druet)
+   * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta)
-  * CBLUP90  - Solutions for bivariate linear-threshold models
+  * 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)
+  * CBLUP90THR - as above but with thresholds computed and many linear traits (B. Auvray)
-  *   CBLUP90REML - as above but with quasi REML (B. Auvray)
+  * CBLUP90REML - as above but with quasi REML (B. Auvray) - no genomic
-  * GIBBSF90 - simple block implementation of Gibbs sampling
+  * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic
-  * GIBBS1F90 - as above but faster because mixed model equations created only once
+  * [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once
-  * GIBBS2F90 - as above but with joint sampling of correlated effects
+  * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects
-  *  GIBBS3F90 - as above with support for heterogeneous residual variances
+  * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances
-  *  POSTGIBBSF90 - graphical tool for post-Gibbs analysis (S. Tsuruta)
+  * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic
-  * THRGIBBSF90 - Gibbs -sampling for any combination of categorical and linear traits (D. Lee)
+  * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic
-  * THRGIBBS1F90 – As above but simplified (S. Tsuruta)
+  * [[readme.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
-  * RENUMF90 -  a renumbering program that also can check pedigrees and assign unknown parent groups; supports large data sets
+  * THRGIBBSF90 - Gibbs sampling for any combination of categorical and linear traits (D. Lee) - no genomic
+  * [[readme.thrgibbs1|THRGIBBS1F90]] - as above but simplified with several options (S. Tsuruta)
+  * [[readme.thrgibbs3|THRGIBBS3F90]] - as above with heterogeneous residual variances for linear traits
+  * [[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.SeekParentf90|SEEKPARENTF90]] -  a program to verify paternity and parent discovery using SNP markers (I. Aguilar)
+  * 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.blupf90new|BLUPF90TEST (new BLUPF90)]] - a combined program of blupf90, remlf90, and airemlf90: under test
+  * [[readme.gibbsf90new|GIBBSF90TEST (new GIBBSF90)]] - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90: under test
 Available by request
-  *   MRF90 - Method R program suitable for very large data sets; contact Tom Druet.
+  * QXPAK - joint analysis of QTL and polygenic effects (M. Perez-Enciso) [[http://www.icrea.cat/Web/OtherSectionViewer.aspx?key=485&titol=Software:Qxpak | QxPak web page]]
-  * COXF90 – Bayesian Cox model - contact Juan Pablo Sanchez  (JuanPablo.Sanchez@irta.cat)
+  * MRF90 - Method R program suitable for a large data set; contact T. Druet.
-  * BLUPF90HYP – BLUPF90 with hypothesis testing  (F  and Chi2 tests) -  contact Juan Pablo as above
+  * COXF90 – Bayesian Cox model - contact J. P. Sanchez (JuanPablo.Sanchez@irta.cat)
+  * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above
 Available only under research agreement
-  *   BLUP90IOD - BLUP by iteration on data with support for very large problems (S. Tsuruta)
+  * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta)
-  *  BLUP90IODTHR - as above for threshold-linear models
+  * BLUP90IOD2R & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances
-  * ACCF90 - approximation of multiple-trait accuracies
+  * [[readme.thr1pcg|CBLUP90IOD]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits)
-  * BLUP90ADJ - Data preadjustment tool
+  * CBLUP90MBE - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits) with support for very large models for multi-breed evaluations
+  * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values
+  * [[readme.accgs|ACCF90GS]] - approximation of accuracies for genomic breeding values
+  * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra)
+  * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool
+  * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2R, and BLUP90IOD2HR: under test
 Included in application programs
-  *   [[readme.pregsf90|PREGSF90]] – genomic preprocessor that combines genomic and pedigree relationships (I. Aguilar)
+  * [[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)
+Other programming contributions were made by Miguel Perez-Enciso ''(user_file)'' and François Guillaume (Jenkins hashing functions).