mothur v.1.6.0

We are happy to announce the release of mothur v.1.6.0 from the new cozy confines of the University of Michigan! Thank you for your patience as we moved the server across the country and then had a hick-up or two while we reconnected everything. Hopefully, by now you have noticed that the picture of my young bride and son have moved to There you can find several useful links - the wiki, a discussion forum, and a link to download mothur. In case you thought we take ourselves too seriously (please see the system command), we have “jumped the shark” and set-up a facebook page for all of the adoring fans. A final bit of very exciting news is that the manuscript describing mothur has been accepted by Applied & Environmental Microbiology. Please cite it liberally. Thanks for the cast of characters that joined me in this venture!

This is a deceptively small update. We have added three commands. First, we have done our best to cull the literature, do some interpretive reading, and implement four algorithms to detect chimeras. The chimera.seqs command implements the Bellerophon, Pintail, CCode, and ChimeraCheck algorithms. Please feel free to play around with these commands and let us know what you think of them. We have had to implement several of these based solely on what was provided in the original manuscript, which didn’t always make sense. If we missed an algorithm, please let us know. Also, the default options in mothur are the way they are implemented in their “home” programs. Second, we have added the align.check command. If you are familiar with the arb editor window, you have noticed that for 16S rRNA sequences they put all sorts of marks under the bases to describe the secondary structure alignment quality. This command will count the number of those different markings for each sequence to allow you to assess alignment quality. Third, we often receive requests from people for something like what we have provided in get.sharedseqs. This command will return the sequences shared between two or more groups. If people still have comments on this command, please let us know. Finally, as we release this version the documentation for these three commands is very sparse. Between the move, setting up the lab, and life the personnel in the documentation department has gotten a little behind. Feel free to take a hack at it if we don’t do it first.

As always we have a number of projects in the works for future releases. These will include taxonomy assignment tools, phylotype-based methods, and OTU-by-OTU comparisons. We are also responding to reviewers’ comments regarding our aligner; hopefully these will be resubmitted in the next week and you will soon see it published in PLoS ONE. As always, thanks for your support and if you have any questions, comments, or critiques, feel free to post them to the forum or to send us an email. I am honestly blown away by the response we have received by users such as yourselves. Remember that our goal is to make this project community-supported and so we’re going to start leaning on you guys to help us out with documentation, answering questions, and providing example analyses.


  • chimera.seqs - a command to detect chimeric sequences using bellerophon, pintail, ccode and chimera check methods.
  • align.check - uses secondary structure maps to check the quality of an alignment.
  • get.sharedseqs - identifies sequences that are shared by multiple OTUs

Bug fixes

  • mothur now checks for empty input files.

Documentation changes

  • mothur forum - please feel free to direct questions to the forum and to answer other people’s questions.
  • publication - the paper describing mothur is now available ahead of print from Applied & Environmental Microbiology. Please cite it!