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Thank you for addressing the reviewer comments.
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.
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.
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?
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