Open Access Open Badges Research

Galaxy tools to study genome diversity

Oscar C Bedoya-Reina1, Aakrosh Ratan12, Richard Burhans1, Hie Lim Kim12, Belinda Giardine1, Cathy Riemer1, Qunhua Li1, Thomas L Olson3, Thomas P Loughran3, Bridgett M vonHoldt4, George H Perry5, Stephan C Schuster12 and Webb Miller12*

Author Affiliations

1 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA

2 Terreus Foundation, 3938 Trust Way, Hayward, CA 94545, USA

3 Penn State Hershey Cancer Institute, Hershey, PA 17033, USA

4 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

5 Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA

For all author emails, please log on.

GigaScience 2013, 2:17  doi:10.1186/2047-217X-2-17

Published: 30 December 2013



Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data.


We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.


This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.

Genome analysis; Species conservation; Population structure; Selective sweeps; Admixture