The paper [Excoffier et al. (2005). Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50, http://www.la-press.com/article.php?article_id=188] provides information on a software tool for population genetics data analysis.

Specific comments:

The article has currently been cited over 11,100 times as per Google Scholar! Its previous version [Schneider et al. (2000). Arlequin ver 2.000: A software for population genetics data analysis. Manual. University of Geneva. 111 pages. http://www.cmpg.unibe.ch/software/arlequin/archive/website/software/2.000/manual/Arlequin.pdf] has been cited over 2298 times (1430 citations until 2005). This fact alone might have influenced the reviewers and the editor to consider the update-article favorably.

While this short (4 pages) application note presents just a new version (3.0) of an existing tool (Arlequin2), it incorporates substantial new features – thus justifying its publication.

The authors were frank by stating in the introduction that “…, Arlequin is a very versatile (though not universal) …”, and “…, but we do not claim that alternative methods implemented by other groups in other programs are inadequate.”

Drawback: The paper (and the associated user manual, http://cmpg.unibe.ch/software/arlequin35/man/Arlequin35.pdf) does not provide information/ examples for novice users on how to use Arlequin 3.0. It only lists key features of the software tool. For example, under “Methods implemented …” section in the article, it has “Search for shared haplotypes between populations” – but the manual does not explain what “shared haplotype” is, and how to “search” for it using an example data.