Review for "Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences"

Completed on 31 May 2018

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Comments to author

This paper is about alignment-free phylogeny reconstruction based on whole-proteome sequences and the authors extend the Filtered Spaced Word Matches to estimate the evolutionary distances between complete or incomplete proteoms and this implementation is called Prot-SpaM.

The proposed method is interesting, and technically-sound and the authors are praised for their work, since their implementation outperforms other alignment-free approaches for calculating the high-quality phylogenetic trees from whole-protome sequences.

Therefore, I recommend accept. Following are some minor comments:

All defied terms and parameters should have consistency. There are some terms which appear both in italic font and simple text font, \textit{i.e.} \textit{homologous}, \textit{spaced-word matches} and \textit{don't-care positions}. Also some words in page 3 are underlined.

Cite Kimura model and PAM distance in line 26 of page 5 should be referenced.

MegaByte shoulb be written as "MB" not "mb".