Mothur

Description

Mothur project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. 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.

License

GNU GENERAL PUBLIC LICENSE version 3

SILVA databases - https://www.arb-silva.de/silva-license-information

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of mothur and load default version of mothur as

module avail mothur/ # list available modules
module load mothur   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail mothur

and choose explicit version you want to use.

Databases are localized in the path /software/mothur/1.42.1/data based on the following licence conditions: https://www.arb-silva.de/silva-license-information (for academic/non-commercial users)

Documentation

Documentation is available at https://mothur.org/wiki/Mothur_manual

Homepage

https://mothur.org/wiki/Main_Page or https://github.com/mothur/mothur