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Versions and Availability


Module Names for paup on qb2
Machine Version Module Name
qb2 4.0 paup/4.0

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.



A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.


System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.


The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.


Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

About the Software

PAUP (Phylogenetic Analysis Using Parsimony) is a widely used software package for the inference of evolutionary trees.


paup requires an input file to define the type of analysis to perform and the data sources to examine.

Use soft-dbq to determine the executable's name:

$ soft-dbq +paup-4.0

This is all the information associated with
the key or macro +paup-4.0.


Name: +paup-4.0
Description: @type: Application/Biology @name: paup @version: 4.0
@about: tools for inferring and interpreting phylogenetic trees
Flags: none
Groups: none
Exists on: Linux


On the Linux architecture,
the following will be done to the environment:

  The following environment changes will be made:
    PATH = ${PATH}:/usr/local/packages/paup/4.0
$ ls /usr/local/packages/paup/4.0
$ paup4b10-opt-linux-a -h
P A U P *
Portable version 4.0b10 for Unix
Mon Mar 31 15:40:51 2014

        This is a beta-test version.  Please report any crashes,
        apparent calculation errors, or other anomalous results.
        There are no restrictions on publication of results obtained
        with this version, but you should check the WWW site
        frequently for bug announcements and/or updated versions.
        See the README file on the distribution media for details.

Usage: paup4b10-opt-linux-a [options...] [input-file-name] [-l log-file-name]
       Options: -a   Append to log-file if already exists
                -r   Replace log-file if already exists
                -n   Run in "non-interactive" mode (no prompts)
                -u   Don't buffer standard output
                -f   Ignore file-locking


Last modified: September 10 2020 11:58:50.