Running PAUP

Author:Brant C. Faircloth
Copyright:This documentation is available under a Creative Commons (CC-BY) license.

Modification History

See Running PAUP


Often, prior to running more computationally intensive analyses of large phylogenies, we’ll take a look at parsimony trees so that we can make sure things are reasonably sensible before moving ahead. These are pretty simple instructions for generating a parsimony tree using PAUP.

Preliminary Steps

  1. Before using PAUP, you need to have the PAUP binary availble on your computer. You can download the binary from here. You can usually do this using a tool like wget. If you are running on our local machines, you will want the CentOS X86_64 version.
  2. Once you have the binary on your computer, you need to make sure it is in your $PATH, and that it is set to be executable. Usually, if you place the binary in $HOME/bin, that will be in your path. Then, you need to chmod 0755 <binary name>.


  1. PAUP requires an input file in NEXUS format. You can produce this in phyluce using:

    phyluce_align_format_nexus_files_for_raxml \
            --alignments mafft-fasta-trimal-clean-75p-complete \
            --output mafft-fasta-trimal-clean-75p-complete-nexus \
  2. Once you have a NEXUS-formatted input file, you need to start PAUP on the command line. Assuming PAUP is in your $PATH, is executable, and is named paup, run:

  3. Then, read in the NEXUS formatted alignment file using:

  4. Set the parsimony criterion, tell PAUP to root on the outgroup, set the outgroup taxon (here, replacing <name_of_tip> with an actualy tip in your tree/alignment):

    set criterion=parsimony;
    set root=outgroup;
    set storebrlens=yes;
    set increase=auto;
    outgroup <name_of_tip>;
  5. Now, run the search; save the results to a file, replacing <output_file_name> with the output tree name you want; and quit:

    hsearch mulTrees=No;
    savetrees file=<output_file_name>.tre format=altnex brlens=yes;