Cool open source software of the month – mothur – for microbial ecology

Anyone interested in microbial ecology informatics should check out the “mothur” software (Main Page – mothur) from Pat Schloss at U. Mass. Schloss, who has developed a lot of great software tools inlcuding for example dotur and sons, is now developing an open source modular sofwate system for microbial ecology studies. And the name of it is mothur (get the theme?). Here is some more detail about mothur:

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. As of version 1.2.0 we have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, and unifrac. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. If you would like to contribute code to the project feel free to download the source code and make your own improvements. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know and we’ll add it to the queue of features we would like to add. Our current goal is to release a new iteration of the project monthly.

Anyway, thanks to my student Amber Hartman for pointing this out — I will be perusing it but thought others should too. Hopefully, we can include some of the software from my lab such as AMPHORA, STAP, etc. into their code at some point.

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

4 thoughts on “Cool open source software of the month – mothur – for microbial ecology”

  1. Thanks for the plug! It's amazing how many people only now get the theme. We'd love to include your stuff – I've been eyeing STAP. Including a classifier function is definitely on the short list of features to add.

    By the way, I just uploaded the manuscript to AEM with about 12 co-authors. Many of whom are junior scientists that I've never actually met. This was an experiment to see how to get people to contribute to an open source project and wiki. The deal was that if they made a significant contribution, they'd be co-authors. Assuming it gets past the reviewers, I'd say it worked. Now to figure out how to keep the momentum going without the stick.


  2. We will be happy contribute and/or use your things.

    As for getting past the reviewers — you really should have submitted this to an Open Access journal … would have been consistent with the Open Source mission.


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