1. In the abstract, the results and conclusion sections are repetitive. The conclusion mentions that this is a "model for development of a Galaxy tool set." However, it reads more like a description of a workflow, not a model of how to go about tool development.

2. Some of the described "tools" are perhaps best described as file manipulations that might be important steps in a particular workflow, but do not stand alone as tools. This is exacerbated because It is not always particularly clear about the big picture questions that are answered by these workflows, although the presentation includes very detailed ways to manipulate very specific files. It would be more useful and clearer to be explicit about what specific evolutionary questions can be answered by the workflow and what specific kinds of data can be used. The example data sets are a start, but require either good knowledge of the context and questions being addressed OR going back to the orginal papers. It would be less burden on the reader if the context were presented more clearly.

3. A small point, but more explicitly, the "phylogenetic trees" distance based.

4. It is somewhat incongruous to complain about not having access to enough datasets to "test the work flows". I would hope that the authors would have more confidence in their tools before publishing. If it is worth publishing these tools, they have to be operational and they make it sound like they don't have enough data on which to test them. People can still use the tools if they are not yet published in some kind of beta form by listing them of the galaxy website. If they ready for publication, then they should be confident in how well tested they are.

5. Some more visuals would be welcome. Given the workflow centric of analyses in the Galaxy platform, some workflow diagrams would complement the descriptions nicely.

Level of interest: An article whose findings are important to those with closely related research interests

Quality of written English: Acceptable

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

Declaration of competing interests: I declare that I have no competing interests