Review History


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Summary

  • The initial submission of this article was received on June 20th, 2017 and was peer-reviewed by 2 reviewers and the Academic Editor.
  • The Academic Editor made their initial decision on July 4th, 2017.
  • The first revision was submitted on July 11th, 2017 and was reviewed by the Academic Editor.
  • The article was Accepted by the Academic Editor on July 15th, 2017.

Version 0.2 (accepted)

· · Academic Editor

Accept

Thank you for addressing the reviewer comments.

Version 0.1 (original submission)

· · Academic Editor

Minor Revisions

This paper has been submitted with external reviews which were taken into account in our decision making process

Please see below the comments of our two reviewers and address the question at the end of Reviewer 2's review. I will accept the paper once I receive the revised version.

·

Basic reporting

No comment.

Experimental design

No comment.

Validity of the findings

No comment.

Comments for the author

Hilton et al. present phydms, a software platform for the analysis of deep mutational scanning data. I have previously reviewed this manuscript with only minor comments, and all comments have been effectively addressed for this PeerJ submission. I have no further comments and I am happy to recommend for publication.

Reviewer 2 ·

Basic reporting

no comment

Experimental design

no comment

Validity of the findings

no comment

Comments for the author

The authors describe a software package that informs phylogenetic analyses with data gathered from deep mutational scanning experiments. The experimentally informed codon model (ExpCM) uses site-specific amino acid preferences from DMS experiments modify the likelihood function for estimating tree branch lengths. This approach provides trees with improved likelihood and AIC. A number of interesting parameters are also estimated from the data including the experimental selection stringency and sites of diversifying selection. Overall, I found the paper to be well written and the methods thoroughly explained. As DMS experiments become more widespread, phydms should be a useful tool for understanding protein phylogeny and evolution.

One specific comment: could the authors please clarify what the last column of Table 1 refers to? Is this the number of sequences in the alignment? If so, these alignments seem a little small?

External reviews were received for this submission. These reviews were used by the Editor when they made their decision, and can be downloaded below.

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