Mailund on the Internet

We just got reviews back from a paper we submitted a few months ago on an algorithmic improvement on the neighbour joining method.  One of them was this:

For large-scale phylogeny reconstruction parsimony and likelihood are the preferred methods. Both are more accurate than neighbor joining (particularly large datasets). It is not clear to me if RapidDiskNJ is a sufficient advance to publish in this journal.

That’s it. The complete review.

Not a single comment on the actual contents of the paper.  Just a blank rejection of the neighbour joining method in general.

And this is an algorithmic improvement.  The paper is on speed and on handling really large data sets, with tens or hundred of thousands of taxa.  Parsemony and likelihood methods simply do not scale to those data sizes.  At least not unless you very large clusters to the problem we solve on a desktop computer.

We improve the speed by several orders of magnitude compared to other implementations of the method, and in comparison with likelihood methods there really is no competition at all.

With reviews like this, peer reviewing just fails!

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