mothur v.1.0.0

February 13, 2009

Hello dotur, sons, slibshuff, and treeclimber users,

We have exciting news to report! Through the funds provided by the NSF and the Sloan foundation, we have begun to develop and release a new program, mothur (i.e. pronounced “mother”). The goal of mothur is to provide a one-stop shop for all of your microbial ecology/environmental microbiology bioinformatics needs. We will be releasing new iterations of mothur on a monthly basis for the next few months until we have all of the basic functionality built into the software. Presently, mothur v.1.0.1 will do the analysis previously done by dotur and sons, plus a few extra bells and whistles. Each month we will be adding a new program as a function within mothur. The March release will enable you do do the parsimony test that was previously handled by treeclimber and some extras. For the time being, we ask that you cite the original dotur, sons, etc. papers until we publish something on mothur.

You can see what we are up to by going to htttp:// and setting up an account on our wiki. While you are free to browse the wiki without an account, you will need to setup an account to download the software. The wiki provides a community-supported manual, information about how we use other software, and details about my availability to lead workshops. I am making myself an open sourced resource - you provide a plane ticket, food, a place to sleep, and the organizational skills to get people together and I’ll yammer on for three days about computational microbial ecology. I call it a bootcamp and it has been successful at the University of Massachusetts, the University of Wisconsin, and in an abbreviated form at the Microbial Diversity course at MBL.

You should definitely consider switching to mothur - if you are analyzing data sets from pyrosequencing or high-throughput Sanger sequencing, you will notice a boost in speed and reduction in memory requirements. mothur is a re-factored version of our previous tools to make use of object-oriented programming and modern design patterns. We hope that if you have the skills, you will consider contributing code to the project. This is an open sourced, community supported, and free software project. We only ask you to set up an account so that we can tell the funding agencies how many users we have and so we can notify you of updates. We are serious about making this a community-supported effort - even if you don’t know how to program, but have an idea, please ask and we’ll add it to the queue of features to add.

Please take mothur for a spin and while we’re sure that your mother doesn’t have any imperfections, this mothur may. So please let us know if you see any differences in output between mothur and our previous software. Finally, thank you all for your continued interest in this software. I started all of this to build a rarefaction curve for a poster and now I’m sending this out to 823 people. Thanks!

All the best, Pat Schloss

PS. If you have access to a windows compiler and would like to compile a windows executable, please let us know.