TreeCluster: clustering biological sequences using phylogenetic trees

PONE-D-19-14871

Dear Dr. Balaban,

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Academic Editor

PLOS ONE

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This manuscript has been corrected since the original GLBIO submission, and still presents a well-reasoned and justified family of methods.

Reviewer #2: The authors considers three versions of clustering sequences based on phylogenies. As they rightly observe, similar problems have been considered in TCS context before, but somehow not used in bioinformatics.

It is good to see that all the problems have linear or near-linear time solutions, although the algorithms themselves use relatively standard algorithmic techniques. The authors also experimentally evaluate their approach in three contexts. I think the results are of sufficient interest for publication in this journal.

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Reviewer #1: No

Reviewer #2: No