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PAUP is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. The program features an extensive selection of analysis options and model choices and accommodates DNA, RNA, protein and general data types. Among the many strengths of the program are the rich array of options for dealing with phylogenetic trees, including importing, combining, comparing, constraining, rooting and testing hypotheses.


A test version of PAUP software is licensed as free software.


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/

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

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

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

module avail paup

and choose explicit version you want to use.

The installed version of PAUP expires every few months. If you need the latest version of this software, install it in your home directory or scratch dir within your batch job according to the following instructions.

  • Download PAUP for Linux (Ubuntu 64-bit version for Debian machines is preferred).

Extract .gz file

gunzip paup4a168_ubuntu64.gz

Make it executable

chmod +x paup4a168_ubuntu64



Optionally you can copy it into ~/bin directory and add a path to the executable binary to your variable $PATH

export PATH=/storage/XXX/home/USER/bin:"${PATH}"