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It would make me cringe if the software names were switched. In full disclosure, my experience with QIIME came from a recent paper I wrote in which we compared various clustering algorithms including those implemented in QIIME.

My hope is that people getting started in the field and that the person that forwarded that reviewer comment to me (and others with similar reiviewers) will find the discussion useful.

I think these analogies reflect the point that a lot of the differences are cosmetic.

Both programs were released within months of each other in 20.

If you are going to campaign for mothur or QIIME, do your best to accurately represent the strengths of your pet package.

When I teach workshops or field users’ questions, I am often asked what I think of QIIME.

As you might expect, the advantage of this approach is that if the developers can write a light wrapper for a new package in Python, then it is pretty painless to bring in other people’s software.

Of course, that software comes in warts and all and creates dependency hell.

Our first draft of any function is to translate the code from its original language to C and make sure we get the same output with the same input. chimera.uchime and metastats) the original authors have made their C code open and we have directly integrated that code into mothur.