Andres Legarra

Drawing

Since 2023 I am Senior Geneticist for CDCB working in genetic evaluation os US dairy cattle. I am also Adjunct (which means no salary and no major duties) Assistant Professor in Animal Genetics and Genomics, University of Georgia.

My work is related to quantitative genetics and genetic evaluation of livestock. E-mail me at andres dot legarra at uscdcb dot com .

I did my PhD in Neiker with Eva Ugarte and I did a postdoc at the Animal and Dairy Science Department at the University of Georgia, with Ignacy Misztal and Keith Bertrand. For 17 years I was Research Director at INRAE Toulouse in the GenPhySE unit, at the Animal Genetics department, and I am now on unpaid leave from INRAE.

This non-fancy web page was created with markdown and MacDown then with the (sadly dead) atom and now Visual Studio Code. I should use vim which is immuable.

You can find in this page links to

My blog with Geekeries and Genetics
My Orcid, Google Scholar, Researcher ID, Researchgate, PubMed and ProdINRA profiles
My github

Software

I have developed my own programs

for genomic prediction GS3 in Github and here with linux, mac, and manual . GS3 was partially financed by Genomia, which was financed by Poctefa.
for variance components in multiple trait threshold models TM source code, Windows executable and manual .

and helped in others’ people programs:

I participate actively in developing the blupf90 family, which now has a wiki and handbook and whose binaries are here.
I have helped a little in developing
- QTL detection software QTLMap
- QTL detection software QxPak
- Simulation software ms2gs

Reviewing

I was (2018-2023) Section, then Senior Editor (Breeding, Genetics, and Genomics) of Journal of Dairy Science
I am Associate Editor of Genetics Selection Evolution

Course on Genomic Selection

This is a course that is taught every two years at UGA, with materials of the 2024 edition . I often teach a part of it. Some materials that we have constructed for this course include notes Bases for Genomic Prediction.

Other material

I chat in Acteon and in bluesky

Notes on Linear Models for Breeding Value prediction (in Spanish)

Fundamentos matematicos de la prediccion de valores de cria.

Francisco Javier Mendizábal Múgica. 1994. Notas de la asignatura Mejora Genética Animal. Escuela Técnica Superior de Ingenieros Agrónomos, UPNA. Pamplona-Iruña, 1994.

I found this very useful to understand linear models, generalized inverses, estimable functions with simple examples. See here: https://github.com/alegarra/Fundamentos/blob/main/capitulo_all.pdf

Genomia

In our POCTEFA grant that what called Genomia, we wrote a document with the state of the art of dairy sheep selection across the Pyrenees. You can find it here.

Metafounders

Our paper in metafounders’ theory contained source code that is lost from the new Genetics site. You cand found this source code here.

I have written a tutorial, here on the use of metafounders to analyse crossbred data with the blupf90 wiki suite using SSGBLUP. The tutorial is conceived for 3-way crosses but the ideas inside can be used (easily) for 2- or 4-way crosses or (a bit more difficult) for complex crosses like in sheep. This work has been financed by Smarter.

Method LR

Similarly, another tutorial here explains the use of method LR to analyze bias and accuracies of evaluation (including genomic prediction). This work has been financed by Smarter.

Quick notes for myself on Julia

Really nothing very sophisticated.

Courses held at GenphySE, INRA

Advanced Quantitative Genetics for Animal Breeding

Taught by Miguel Angel Toro, Universidad Politecnica de Madrid at GenPhySE, INRA Toulouse March 14-17, 2017. Slides are here.

Systems Biology and Gene Networks Inference: Application to Livestock Breeding and Genetics

Taught by Toni Reverter, CSIRO Agriculture and Food, Brisbane, Australia at GenPhySE, INRA Toulouse, Nov 19-23, 2018. All slides are here.

Some other documents

My 2002 PhD dissertation (in Spanish)
My 2012 HDR dissertation (in French)

and, in English: