Summary:

This is fantastic work that combines novel biological and computational elements to (i) make genome diversity tools widely available via the Galaxy platform and (ii) demonstrate how these tools can be used to understand genome diversity both within and across species.

Major Compulsory Revisions:

None

Minor Essential Revisions:

1. Chicken section: some correlation metric should be used to determine how similar the authors' results to Rubin et al. (2010). The discussion of individual data points is great, but overall correlation is important as well. A Spearman rank using region score may work well, but the authors should do what they believe is best.

2. A Galaxy page that links to datasets and workflows used in this paper (perhaps this is what the URL usegalaxy.org/r/diversity-tools is for?) together with the tutorials hosted on the Miller lab website. The page can serve as a landing spot for readers that want to view the materials for or do any of the analyses described in the paper. The workflows should also be included in the tools' repository on the toolshed.

3. Page 4: "This is the status as of July, 2012" -- should this be July, 2013?

Discretionary Revisions:

1. Running the tools requires quite a bit of software according to the README in the toolshed repository. It would be nice to take advantage of toolshed features to automatically install some of this software: http://wiki.galaxyproject.org/DefiningRepositoryDependencies

Level of interest: An article of importance in its field

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: I am a member of the Galaxy team and employed through grants to the Galaxy project. The Galaxy project, and myself, may see a small benefit if this article is published. The potential benefit would be increased reputation of Galaxy in the scholarly community; neither myself nor the Galaxy project would receive any monetary benefits.