BLUPF90 manual is available at BLUPF90 manual
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.
A tutorial of BLUPF90 programs is available as Introduction to BLUPF90 suite programs.
Another more specific tutorial concerns the use of blupf90 software to analyze crosses using the theory of metafounders and SSGBLUP, and it is available at (http://genoweb.toulouse.inra.fr/~alegarra/ThreeWayDist/crosses_blupf90.pdf).
The following is the original documentation of our programs. The manual has the same information.
BLUPF90, and the kind of models that can be fit: blupf90.pdf.
Those interested in programming can access notes from a computing class in Fortran 95.
READMEs and documentation are hard to follow without an understanding of Mixed Models as applied to Animal Breeding. A free, highly recommended material is Larry Schaeffer's notes.