BLUPF90
family of programs is a collection of software in Fortran 90/95 for
mixed model computations in animal breeding. The goal of the software is to be
as simple as with a matrix package and as efficient as in a programming
language. For general description, see a paper from the CCB'99
workshop, or see a paper on BGF90 at 7th WCGALP.
For
variance component estimation, the family offers choices for simple and
complicated models; see paper “Reliable
computing in estimation of variance components”. From 2009 the programs are
successively modified for genomic selection using a single-step
approach (or ssGBLUP) by Ignacio Aguilar and
Shogo Tsuruta.
The family contains:
Modules
Application
programs
They support mixed models with
multiple-correlated effects, multiple animal models and dominance.
o BLUPF90
- BLUP in memory
o REMLF90 -
accelerated EM REML
o QXPAK -
joint analysis of QTL and polygenic effects (M. Perez-Enciso)
o AIREMLF90 -
Average Information REML (S. Tsuruta)
o AIREMLRES - as
above with support for heterogeneous residual variances (T. Druet)
o CBLUP90 -
Solutions for bivariate linear-threshold models
o CBLUP90THR
-as above but with thresholds computed and many linear traits (B. Auvray)
o CBLUP90REML -
as above but with quasi REML (B. Auvray)
o GIBBSF90 -
simple block implementation of Gibbs sampling
o GIBBS1F90 - as
above but faster because mixed model equations created only once
o GIBBS2F90 - as
above but with joint sampling of correlated effects
o GIBBS3F90 - as
above with support for heterogeneous residual variances
o POSTGIBBSF90 -
graphical tool for post-Gibbs analysis (S. Tsuruta)
o THRGIBBSF90 -
Gibbs -sampling for any combination of categorical and linear traits (D. Lee)
o THRGIBBS1F90
– As above but simplified (
o RENUMF90
- a renumbering
program that also can check pedigrees and assign unknown parent groups;
supports large data sets
o
Available
by request
o MRF90 - Method
R program suitable for very large data sets; contact Tom Druet.
o COXF90 –
Bayesian Cox model - contact Juan Pablo Sanchez (JuanPablo.Sanchez@irta.cat)
o BLUPF90HYP –
BLUPF90 with hypothesis testing (F and Chi2 tests) - contact Juan Pablo as above
o
Available
only under research agreement
o BLUP90IOD -
BLUP by iteration on data with support for very large problems (S. Tsuruta)
o BLUP90IODTHR -
as above for threshold-linear models
o ACCF90 -
approximation of multiple-trait accuracies
o BLUP90ADJ -
Data preadjustment tool
o
Included
in application programs
o PREGSF90
– genomic preprocessor that combines genomic and pedigree relationships
(I. Aguilar)
Documentation
Some
documentation is available as README files in source directories. See comments on
properties of some of the programs. See Shogo Tsuruta’s
pages for FAQ and
individual comments
on each program. Those interested in programming can access notes from a computing class
in Fortran 95.
Condition of use
The
programs are free for research but their use should be acknowledged in
publications.
Distribution
Sources
Older
versions are available as Fortran 95 package for
download and compilation on Unix systems. Various problems were reported using
free Fortran compilers. At this time, the best compiler appears to be from
Intel; it is free for noncommercial use in Linux.
Linux
and Mac binaries and Windows executables
Binaries for Linux, Windows and Mac are here. File blupf90_win.zip
contains Windows
executables + GNUPLOT; an included script file sets access to all binaries and
the graphing package.
Support
Limited
assistance is provided by Shogo
Tsuruta, Ignacio
Aguilar, Ignacy Misztal.
Genomic support is mainly by Yahoo group blupf90
– sign up at http://tech.groups.yahoo.com/group/blupf90/. For more
extensive assistance consider a visit to UGA.