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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.In fact, you can actually run mothur from within QIIME.It’s a very old version of mothur, but you can use mothur to cluster sequences in QIIME.

When you run classify.seqs, you are not running the code developed by the RDP.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.When I’ve heard QIIME developers talk at conferences, one comment they make is that they allow people to use methods the way it was originally implemented. At the same time, if you told people that you had to use Gosset’s original implementation of Student’s T-test and it couldn’t be ported to SAS, SPSS, R, Excel, etc. I would be curious to know how much dead wood exists in QIIME - I could foresee functions that were developed by a contributor that then graduate or lose interest and there is no one left to maintain or update the code.The QIIME development team may have a mechanism to deal with this type of problem, but the fact that they are using mothur v1.25, which was released in May 2012, suggests that there is some slippage.

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