Welcome to the website for the mothur project, initiated by Dr. Patrick Schloss and his software development team 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. Since then we have added the functionality of a number of other popular tools including s-libshuff, TreeClimber (i.e. the parsimony test), UniFrac, distance calculation, visualization tools, a NAST-based aligner, and many other features. 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.