Phylogenetics: Introduction to PAUP*

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Adiantum.png EEB 5349: Phylogenetics

Using PAUP to create a NEXUS data file


Now login to the cluster ( and type paup to start the PAUP* program.

Important! Ordinarily, you should not run PAUP* directly like this. Only use this method for extremely short-lived activities. To run an analysis on the cluster, 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 a good way to annoy your colleagues! That said, what we are doing today will not be computationally demanding and thus should not cause any noticeable slowdown for other cluster users.

Now type in the following (PAUP) command:



Automatically excluding sites using a default exset


begin assumptions;


Defining sets of sites

Create a sets block comprising the following three charset commands:




paup angio35.nex


exclude all;
include rbcL;


include 18S atpB;


Setting up a log file


log file=output.txt start replace;

Getting help



Performing a parsimony search


What was PAUP*'s response to this request?



Showing and saving trees


outgroup 1-7;


set torder=right;


savetrees file=pars.tre brlens;

Scoring trees using the likelihood criterion


set criterion=likelihood;
lscores all;




Comparing NJ to parsimony and likelihood




lscores all;


pscores all;

Closing down


log stop;


Sets block

The only commands you need to know at this point from a sets block are the charset and the taxset commands.

begin sets;
  charset trnL_intron = 562-4226;
  taxset gnetales = Ephedra Gnetum Welwitschia;

This sets block defines both a set of characters (in this case the sites composing the trnL intron) and a set of taxa (consisting of the three genera in the seed plant order Gnetales: Ephedra, Gnetum and Welwitschia). We could have used the taxon numbers for the taxset definition (e.g., taxset gnetales = 1-3;) but using the actual names is clearer and less prone to error (just think of what might happen if you decided to reorder your sequences!). These definitions may be used in other blocks. A common use is in commands placed inside a paup block (see below) or typed directly at the PAUP* command prompt.