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”. Beginning in 2009, the
programs are successively modified for genomic selection using a single-step
approach by Ignacio Aguilar.
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
Available by request
o
MRF90 - Method
R program suitable for very large data sets; contact Tom Druet.
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
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.
Distribution
Sources
Most programs 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. Compilers from Absoft and Lahey worked as
well.
Linux binaries and Windows
executables
Most programs are precompiled as Linux binaries or Windows executables. 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, and Ignacy Misztal. For more extensive
assistance please consider a visit to UGA.