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About this tutorial

General information

Purpose

This document explains how to describe a model in a parameter file used with the BLUPF90 family of programs, how to prepare data and pedigree files, and how to perform genomic analyses with the programs. This tutorial assumes that the reader has sufficient knowledge of linear mixed models and data-manipulation techniques. Experience with similar software will also be helpful for understanding the content.

The features of the BLUPF90 programs are introduced in an introductory style. In particular, the first section of each chapter presents essential features using a very simple example. Later sections introduce new concepts through more practical examples. We recommend that readers do not skip any sections, even if they seem too elementary.

This tutorial complements the official manual and wiki pages. Because the official manual serves primarily as a reference, it presents each topic concisely. For advanced topics or technical tricks, please refer to the manual. Conversely, if you find that something is missing in the manual, this tutorial may help you understand the background. If you have a question that is not addressed in the manual, the wiki, or this tutorial, please ask in the Yahoo Group (https://groups.yahoo.com/neo/groups/blupf90/info). You may find answers in the historical discussion logs of the forum.

About the author

The original author is Yutaka Masuda. The initial version of this tutorial was written while the author was working as a research scientist in the Animal Breeding and Genetics group at the University of Georgia (UGA). The author modified the source code of BLUPF90 and incorporated new computational ideas into the programs at UGA. Even after leaving that position, the author occasionally updated this tutorial.

The current version of this tutorial (version 1.9.0 or later) is now the author’s personal project and is unrelated to his current affiliation or the UGA group. The new descriptions introduced in this version are based on publicly available information and the author’s own research on the BLUPF90 programs. This tutorial is not an official document published by UGA. However, the UGA team is aware that the original author continues to maintain and update the tutorial. The author believes that it is still useful and mostly correct in its descriptions of the BLUPF90 family of programs. In addition, this tutorial uses “we” or “us,” even though the author is no longer part of the team. Please disregard this use of the pronoun; it is retained for historical reasons.

Examples in each section

Example data

In each section, I provide various examples for the reader. The files are available in the author’s GitHub repository (https://github.com/masuday/data). Examples in this tutorial are enclosed in a frame, as shown below.

1   1   2.5
2   1   1.8
3   1   4.2
4   1   2.2
5   1   3.6

Parameter file for BLUPF90

Parameter files used in the BLUPF90 programs are highlighted as follows.

# This is a BLUPF90 parameter file.
DATAFILE
data0.txt
NUMBER_OF_TRAITS
1
NUMBER_OF_EFFECTS
1
OBSERVATION(S)
1
WEIGHT(S)

EFFECTS:
2 3 cross
RANDOM_RESIDUAL VALUES
1.0

Parameter file for renumbering by RENUMF90

Alternative parameter files used in RENUMF90 (referred to as instruction files in this tutorial) are shown as follows.

# This is an example of a renum-parameter file.
DATAFILE
rawdata1.txt
TRAITS
5
FIELDS_PASSED TO OUTPUT

WEIGHT(S)

RESIDUAL_VARIANCE
1.0
EFFECT          # 1st effect
2 cross alpha
EFFECT          # 2nd effect
3 cross alpha
EFFECT          # 3rd effect
4 cov

Output

The output from the programs is shown in a different format.

 name of parameter file?

Commands on shell

If you need to type a command in your shell (terminal or Command Prompt), the command line is shown as follows.

./airemlf90 renf90.par

Disclaimer

The following disclaimer is based on the MIT License, although this tutorial is distributed under the Creative Commons BY-NC-ND 4.0 International license.

This tutorial is provided “as is”, without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the tutorial or the use or other dealings in the tutorial.

I wrote this documentation in Markdown using Pandoc extensions. The PDF file is generated using Pandoc, so there may be typesetting or layout issues.

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