Differences

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--- application_programs [2022/05/10 21:48] – dani
+++ application_programs [2024/06/19 14:22] (current) – andres
@@ Line 3: / Line 3: @@
 **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_all8.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. ''inbupgf90'')
+Download {{:blupf90_ALL.pdf|BLUPF90 family manual}}. Note that some programs shown below are not in the manual (e.g. ''inbupgf90'')
+\\
+How to cite the BLUPF90 manual:
+Misztal I., Tsuruta S., Lourenco D.A.L., Aguilar I., Legarra A., and Vitezica Z. 2014. Manual for BLUPF90 family of programs.
 \\
 ===== Programs =====
-**Available for research (free)**
+**Available for research (free with restriction: # genotyped animals = 25,000)**
   * [[readme.blupf90plus|BLUPF90+]] - a combined program of blupf90, remlf90, and airemlf90
   * [[readme.gibbsf90plus|GIBBSF90+]] - a combined program of gibbs1f90, gibbs2f90, gibbs3f90, thrgibbs1f90, and thrgibbs3f90
@@ Line 19: / Line 24: @@
   * [[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)
+  * [[Readme.validationf90|VALIDATIONF90]] -  a program to perform validation of predictions (coming soon!)
+  * [[Readme.rrmebvf90|RRMEBVF90]] -  postprocessor for random regression models (coming soon!)
 /*Included in application programs*/
@@ Line 30: / Line 37: @@
 **Available only under research agreement**
   * [[readme.pcg2|BLUP90IOD2]] - BLUP by iteration on data with PCG for very large models (S. Tsuruta)
-  * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90)
+  * [[readme.pcgtest|BLUP90IOD3 (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR,  BLUP90IOD2HR, and BLUP90MBE2 with new features
   * [[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
   * [[readme.acc|ACCF90]] - approximation of accuracies for breeding values
-  * [[readme.accgs|ACCF90GS]] - approximation of accuracies for genomic breeding values
+  * [[readme.accgs|ACCF90GS]] - approximation of accuracies for genomic breeding values based on diagonals of **G**
-  * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra)
+  * [[readme.accgs2|ACCF90GS2]] - new approximation of accuracies for genomic breeding values based on block sparse inversion
   * [[readme.blupadj|BLUP90ADJ]] - BLUP data preadjustment tool
   * [[readme.deproofs|DEPROOFSF90]] - computation of deregressed proof (DRP)
   * [[readme.dyd|DYDF90]] - computation of daughter yield deviation (DYD) known as progeny trait deviation
-  * [[readme.pcgtest|BLUP90IODTEST (new BLUP90IOD)]] - a combined program of BLUP90IOD2, BLUP90IOD2RR, and BLUP90IOD2HR: under test
 **No longer updated (as of May 2022)**
@@ Line 57: / Line 64: @@
   * [[readme.gibbscen|GIBBS2CEN]] - support censored data (J. Arango) - no genomic
   * [[readme.gibbsrecur|GIBBS2RECUR]] - support recursive models (J. P. Sanchez) - no genomic
+  * BLUP90IOD2RR & BLUP90IOD2HR - BLUP90IOD2 with heterogeneous residual variances (like in GIBBS3F90 & AIREMLF90)
+  * BLUP90MBE - BLUP by iteration on data with support for very large models for multi-breed evaluations (A. Legarra)
 Other programming contributions were made by Miguel Perez-Enciso ''(user_file)'' and François Guillaume (Jenkins hashing functions).