Mothur provides microbial ecologists with the functionality of dotur, sons, treeclimber, s-libshuff, unifrac and more.

Mothur is a project initiated by Dr. Patrick Schloss. It is a single piece of software that incorporates the functionality of dotur, sons, treeclimber, s-libshuff, uni frac and more. In essense, the goal of mothur is to provide a single resource to analyse molecular data used by microbial ecologists.

Functionality includes sequence processing, allowing you to go from Sanger sequences or pyrosequences to a distance matrix, carry out OTU-based approaches and hypothes is testing appropaches in considering the frequency distribution of sequences found in bins.

As of version 1.11 on Bio-Linux, mothur can run under mpi, which allows you to make use of multiple cores. To run mothur under mpi, you could use a command like:

The above would run mothur making use of 2 cpu, assuming two are available.

To run commands under mpirun, you need to have mpd running on your system. So the full set of commands you might need to run, if mpd is not already set up and running, is below. (Replace the word secret with an actual, secret password.)