|Author:||Brant C. Faircloth|
|Copyright:||This documentation is available under a Creative Commons (CC-BY) license.|
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.
- 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.
- 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>.
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 \ --nexus
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
Then, read in the NEXUS formatted alignment file using:
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>;
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; quit;