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About the software

Condition of use

For detailed information about the conditions of use and support, please visit the official wiki (http://nce.ads.uga.edu/wiki/doku.php). The programs are free for research use, but publications should acknowledge the use of the programs. Please contact the UGA faculty (see http://nce.ads.uga.edu/ for contact information).

Bug report and support

Bug reports are welcome. Please contact one of the developers at UGA or other institutes, or post your report on Groups.io (https://groups.io/g/blupf90). Support may be limited on Groups.io because it is provided on a volunteer basis. Note that we have moved from Yahoo Groups to Groups.io due to changes in Yahoo’s policy. If you need full support for the programs, please consider visiting our team.

Citations

You can cite the following publication when you use the BLUPF90 programs in your study. Please note that this manual is occasionally updated, but you can cite the version published in 2014.

• Misztal, I., S. Tsuruta, D. A. L. Lourenco, Y. Masuda, I. Aguilar, A. Legarra, Z. Vitezica. 2014. Manual for BLUPF90 family programs. University of Georgia. http://nce.ads.uga.edu/wiki/doku.php?id=documentation (This is the standard reference usually cited by users.)

If you cite this tutorial in your publication, please use the following reference in addition to the manual listed above. Please also note that you may cite the original version of the tutorial published in 2018, although it has been revised several times in the past and may be updated again in the future.

• Masuda, Y. 2018. Introduction to BLUPF90 suite programs. University of Georgia. http://nce.ads.uga.edu/wiki/doku.php?id=documentation

If you need to cite a particular feature of the BLUPF90 programs, the following references may be useful. Please be aware that new articles on this topic may be published in the future, and you are encouraged to cite the most recent one in your publications.

• Lourenco, D. A. L., Tsuruta, S., Masuda, Y., Bermann, M., Legarra, A., Misztal, I. Recent updates in the BLUPF90 software suite. In: Proceedings of the 12th World Congress on Genetics Applied to Livestock Production; 2022 July 3-8; Rotterdam.

• Lourenco, D. A. L., Legarra, A., Tsuruta, S., Masuda, Y., Aguilar, A., Misztal, I. 2020. SingleStep Genomic Evaluations from Theory to Practice: Using SNP Chips and Sequence Data in BLUPF90. Genes, 11:790. https://doi.org/10.3390/genes11070790

The following references are older, but they may still be useful for referring to specific features of the program.

• Aguilar, I., S. Tsuruta, Y. Masuda, D. A. L. Lourenco, A. Legarra, I. Misztal. 2018. BLUPF90 suite of programs for animal breeding with focus on genomics. No. 11.751. The 11th World Congress of Genetics Applied to Livestock Production, Auckland, New Zealand. (This is the most recent reference for BLUPF90 programs focusing on genomic analysis.)

• Aguilar, I., I. Misztal, S. Tsuruta, A. Legarra, H. Wang. 2014. PREGSF90 - POSTGSF90: Computational Tools for the Implementation of Single-step Genomic Selection and Genome-wide Association with Ungenotyped Individuals in BLUPF90 Programs. The 10th World Congress of Genetics Applied to Livestock Production, Vancouver, BC, Canada. (This can be cited if you used a combination of PREGSF90 and POSTGSF90 to perform single-step GWAS.)

• Misztal, I., S. Tsuruta, T. Strabel, B. Auvray, T. Druet, D. H. Lee. 2002. BLUPF90 and related programs (BGF90). Communication No. 28-07. The 7th World Congress on Genetics Applied to Livestock Production, August 19–23, 2002, Montpellier, France. (This was widely cited in the past, but is now considered outdated. Use this reference only if you have a specific reason.)

The following reference is cited in the technical descriptions in the subsequent chapters:

• Misztal, I. 2024. Computational techniques in animal breeding. Course Note. University of Georgia.

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