Lab #2 Parsimony analysis with PAUP and TNT

The objective of this lab is to learn how to do a parsimony analysis using PAUP and TNT. We will also review how to align molecular sequences with MAFFT.

First things first

Modifying the PATH Variable

The PATH environment variable is a colon-delimited list of directories that your shell searches through when you enter a command. Your path tells the Unix shell where to look on the system when you request a particular program. To find out what your path is, at the Unix shell prompt, enter: echo $PATH. I have installed PAUP and TNT in a shared directory for the class (/work/class-faculty/dlavrov/eeob563/bin). While you can run these programs by using the full path name: /work/class-faculty/dlavrov/eeob563/bin/paup, it’s easer to add this directory to the path:

1. Add /work/class-faculty/dlavrov/eeob563/bin directory to your path:
   • Log in to Nova using ssh <netID>@nova.its.iastate.edu command.
   • Open your bash profile file in vi: vi ~/.bash_profile;
   • Go to the PATH=... line using the down arrow;
   • type A (for add) and add the following text to the end of the line: :/work/class-faculty/dlavrov/eeob563/bin
   • press ESC
   • type ZZ (or :wq) to save and quit the file;
2. Run source ~/.bashrc;
3. Type paup to make sure that you can run the program;
4. Type q to quit PAUP.

Working on the HPC-class partition

When you log in to a computer cluster you enter the “head node”. This node is shared with all the other users of the cluster. To “reserve” a “private” node, use the salloc -p class-long -N 1 -n 2 -t 2:00:00 -A s2023.eeob.563.1 command. Running programs on this node will not interfere with the other work on the cluster.

Updating the class repository

We also need to update the class repository and go to the proper directory:

• cd EEOB563-Spring2023; git pull)
• cd computer_labs/lab2.

IMPORTANT: It is likely that NOVA won’t be available on Feb. 07. We will do PAUP exercise on our personal computers!

Download PAUP from its website: https://paup.phylosolutions.com

PAUP

PAUP tutorial

TNT (optional)

TNT tutorial If you like a challenge you can try TNT with the dinosaurs data

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