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application_programs [2022/05/04 23:53] – daniapplication_programs [2022/05/10 21:00] – dani
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 **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> **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>
  
-Download {{:blupf90_all7.pdf|BLUPF90 family manual}}. Note that some programs repertoried below are not in the manual (e.g. ''inbupgf90'')+Download {{:blupf90_all7.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. ''inbupgf90'')
  
-   * [[readme.blupf90|BLUPF90]] - BLUP in memory +\\ 
-   * [[readme.reml|REMLF90]] - accelerated EM REML +**Main programs** 
-   * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) +  * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 
-  * CBLUP90  - solutions for bivariate linear-threshold models (works only for 2 trait model: threshold and linear) +  * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
-  * 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.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic +
-  * [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once +
-  * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects +
-  * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances +
-  * [[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.postgibbs|POSTGIBBSF90]] - statistics and graphics for post-Gibbs analysis (S. Tsuruta)
-  * 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.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)   * [[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.qcf90|QCF90]] - a quality-control tool on genotypes and pedigree information (Y. Masuda)
-  * [[readme.blupf90new|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90 +  * [[Readme.Inbupgf90|INBUPGF90]] - a program to calculate inbreeding coefficients with incomplete pedigree (I. Aguilar)  
-  * [[readme.gibbsf90new|GIBBSF90+]] - a combined program of gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90 +  * [[Readme.SeekParentf90|SEEKPARENTF90]] -  a program to verify paternity and parent discovery using SNP markers (I. Aguilar) 
-  + 
-Available by request+/*Included in application programs*/ 
 + 
 +**Available by request**
   * 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]]   * 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]]
   * MRF90 - Method R program suitable for a large data set; contact T. Druet.   * MRF90 - Method R program suitable for a large data set; contact T. Druet.
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   * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above   * BLUPF90HYP – BLUPF90 with hypothesis testing (F and Chi2 tests) - contact J. P. Sanchez as above
      
-Available only under research agreement+**Available only under a research agreement**
   * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta)   * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta)
-  * BLUP90IOD2R & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances+  * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90)
   * [[readme.thr1pcg|CBLUP90IOD2]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits)   * [[readme.thr1pcg|CBLUP90IOD2]] - BLUP by iteration on data for threshold-linear models (working for one threshold and several linear traits)
   * 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   * 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
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   * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP)   * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP)
   * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation   * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation
-  * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2R, and BLUP90IOD2HR: under test+  * [[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.blupf90|BLUPF90]] - BLUP in memory 
-  * [[readme.pregsf90|POSTGSF90]] – genomic postprocessor that extracts SNP solutions after genomic evaluations (single step, GBLUP) (I. Aguilar)+  * [[readme.reml|REMLF90]] - accelerated EM REML 
 +  * [[readme.aireml|AIREMLF90]] - Average Information REML with several options including EM-REML and heterogeneous residual variances (S. Tsuruta) 
 +  * [[readme.gibbs|GIBBSF90]] - simple block implementation of Gibbs sampling - no genomic 
 +  * [[readme.gibbs1|GIBBS1F90]] - as above but faster for creating mixed model equations only once 
 +  * [[readme.gibbs2|GIBBS2F90]] - as above but with joint sampling of correlated effects 
 +  * [[readme.gibbs3|GIBBS3F90]] - as above with support for heterogeneous residual variances 
 +  * 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 
 +  * 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). Other programming contributions were made by Miguel Perez-Enciso ''(user_file)'' and François Guillaume (Jenkins hashing functions).
application_programs.txt · Last modified: 2024/06/19 14:22 by andres
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