Welcome to the website for the mothur project, initiated by Dr. Patrick Schloss and his research group in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. In February 2009 we released the first version of mothur, which had accelerated versions of the popular DOTUR and SONS programs. The paper announcing mothur’s release has gone on to become one of the most cited bioinformatics tool for analyzing 16S rRNA gene sequences. Be sure to read the 2020 retrospective on mothur’s development over the previous 10 years and where it hopes to go in the future. Step inside the wiki and user forum to learn how you can use mothur to process your amplicon sequence data.

If you would like to contribute documentation, feel free to use the links to the right of each page to improve the text or raise questions about things that are not clear. Have an idea for a new feature in mothur or for something that would improve an existing feature? Feel free to download the source code, make your improvements, and ask us to fold those changes into the existing code. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know through the forum and we’ll add it to the queue of features we would like to add. Be sure to subscribe to the mothur mailing list so that you can be updated on any new releases and upcoming workshops!