Post-Alignment Adjustment and Its Automation

Round 1

Reviewer 1 Report

The author describes the problems generated by alignment error very clearly and offers a convincing and pedagogic case for position weight matrix as a method to correct common alignment errors in progressive multiple sequence alignments. Aside from the language suggestions I have provided in the attached annotated PDF document, I cannot propose any changes to improve this manuscript.

Comments for author File: Comments.pdf

Author Response

I am very grateful to the reviewer for patient editing of my manuscript. I have accepted all recommendations in the annotated PDF file from the reviewer. The changes dramatically improved the readability of the manuscript.

Reviewer 2 Report

This work brings attention to the important of the MSA in accurately inferring phylogenetic trees, and associated biases. The author reviews three different methods for evaluating suboptimal sites and readjustment after the alignment, and emphasise on the utility of the position weight matrix (PWM) as a new tool for multiple sequence refinement. There are practical and real biological examples throughput the text, which helps to understand the algorithm behind each method. Although, at this stage no new computational software for this purpose has been developed, but this research brings up the importance of the post-alignment and the biases associated with different methods, opening the way for developers to investigate this area, and hopefully we see new algorithms/software with more sensitivity and accuracy in MSA.

I enjoyed reading the manuscript, and although have no particular comment to improve the manuscript I can see the potential impact on the rapidly developing genomic field.

Author Response

I thank the reviewer for the encouraging words.