Phylogenetics: NEXUS Format

	EEB 349: Phylogenetics
	The goal of this lab exercise is to show you how to easily create a NEXUS-formatted data file from a set of sequences. The NEXUS format is widely used in phylogenetics, and its basic features are described in the second part of this tutorial.

Using PAUP to create a NEXUS data file

First, download the file angio35.nex to your hard drive and then upload it to the cluster (instructions in Phylogenetics: Bioinformatics Cluster).

Now login to the cluster (bbcxsrv1.biotech.uconn.edu) and type paup to start the PAUP* program.

Important! Ordinarily, you should not run PAUP* this way. Only use this method for extremely short-lived activities. To run an analysis on the cluster (that will take 10 minutes or longer), you should use the Sun Grid Engine's qsub program to submit a job. Using qsub starts your run on one of the computing nodes (whichever is free at the moment), while typing paup starts PAUP* on the head node, which is the node that everyone logs into to start runs. Bogging down the head node with a long PAUP* run is the quickest way to lose your cluster privileges! That said, what we are doing today will not be computationally demanding and thus should not attract the attention of Jeff Lary (if it does, I will take the blame).