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PAUPRat on the cluster

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A script is available on the cluster that takes some of the work out of running a PAUP ratchet analysis. This script implements parsimony ratchet analyses using PAUP and PAUPRat (a program written by Derek S. Sikes and Paul O. Lewis).

See these references for background on the methodology:

• Goloboff, P. 1999. Analyzing large data sets in reasonable times: Solutions for composite optima. Cladistics 15: 415-428.
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• Nixon, K. C. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
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• Sikes, D. S. and P. O. Lewis. PAUPRat manual.
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• Swofford, D. L. 1998. PAUP* Phylogenetic analysis using parsimony (*and other methods), 4.0b4a. Sinauer Associates, Sunderland, Massachusetts.

The script will run the PAUP ratchet on the cluster - sending each ratchet analysis to a different node. For example if you do 20 runs each with 200 iterations, each of your 20 runs will be on a different node. The script will also create the subdirectories and files needed to do multiple runs.

To use the script:

1. Place your nexus data file (with UNIX line breaks) into an empty directory and change into (cd) this directory.
2. 
   
3. To start your analyses, type "runrat.paup". You will be asked for the name of your data file, the number of characters in your data set, and how many ratchet runs you want to do. You will then be asked if you want to change the default number of iterations and percent of characters perturbed. If you choose "no", the script does its thing, but if you choose "yes", you can specify whatever you want. The script does everything else.
4. 
   
5. Emails will be sent to your UMSL account indicating when your individual runs have completed.
6. 
   
7. To collect all of the trees from the indepent runs into a single file, change into (cd) the directory containing all of the run folders and type "collectrees.pauprat". You will be asked for the number of indepent runs that you performed and to designate a name for the output tree file. You can import these trees directly into PAUP and then filter to keep the shortest length trees.