Thanks for sending me the manuscript titled “OPTIMA: Sensitive and accurate whole-genome alignment …”. The authors developed an alignment algorithm that is more efficient, sensitive and precise, when benchmarked against several existing computational tools.

Major Revisions:
1. Detailed instructions of how to run the program should be provided, including command lines, parameters and input/output file format.
2. The simulated dataset and real world dataset used in this manuscript should be accessible for users and reviewers to reproduce results presented by the authors.
3. In Figure 2, it seems that single match outperforms all other seeding methods. So a naïve question is, why didn’t the authors use single match?
Minor Revision:
1. In almost all Figures, the size of the black solid line box should be adjusted.

Level of interest An article of importance in its field
Quality of written English Acceptable
Statistical review Yes, but I do not feel adequately qualified to assess the statistics.
Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/1163627124192524_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/8481523751718841_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/8481523751718841_manuscript.pdf

I have no more concern.
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 declare that I have no competing interests.

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1969015422193583_manuscript.pdf
All revised versions are also available:
First revision - http://www.gigasciencejournal.com/imedia/1969015422193583_manuscript.pdf