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Third Party Analysis Scripts/Programs

If you develop a script (e.g., Perl or Python) or program to parse and analyze character histories, or anything else that would useful to SIMMAP users or generally anything phylogenetic, and would be willing to share them I would be willing to distribute them through this web site or provide a link to an external download site. The only requirements I have for distributing a script/program is that it is relevant to phylogenetics and that you, the author, identify yourself with contact information for users.

If you would like to contribute feel free to contact me at:



Please don't use this web site as the sole link or repository for published scripts.

Disclaimer

The scripts/programs below are provided as a courtesy and the author of SIMMAP, Jonathan P. Bollback, is not responsible for their accuracy, quality or performance. Some of the scripts may contain a License, please read before using. If you have problems with a script please contact the author directly unless the script is developed by J.P.B.

If you use one of these scripts in a publication please cite the author in an appropriate fashion by contacting the author first. Do not use this as the weblink for a script in a publication.

Descriptions:
  1. resolve.zip: A Python script for randomly resolving tree polytomies. It reads in a single tree and lets the user define the number of random resolutions desired and the branch length to assign to the resolved branches. To use this script to allow trees with polytomies to be read by SIMMAP simply set the branch length to 0.0 and do a single resolution. The resulting tree can then be used by SIMMAP to accommodate polytomies.

  2. splitpossel.zip: A Python script that reads in a Nexus tree file containing synonymous and non-synonymous trees, with the number of changes as branch lengths, generated by SIMMAP during a codon analysis. The script writes out two files parsing them into synonymous and non-synonymous tree files. These can be used to read into a program like MrBayes to, for example, obtain consensus trees or explore different aspects of molecular evolution.

  3. convert2tracer.zip: A Python script that reads in the individual statistics file produced by SIMMAP and reformats it so that it can be read into the program Tracer. Tracer allows you to visualize the posterior distributions sampled by SIMMAP. As always check that the converted file looks correct.

Downloads:

File Type Version Last Updated Author Size    
resolve.zip Python 0.1 13.04.2006 J.P.B. 5 KB Download
splitpossel.zip Python 0.1 19.04.2006 J.P.B. 4 KB Download
convert2tracer.zip Python 0.2 28.08.2008 J.P.B. 4 KB Download


    
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Page Last Updated: 6 August 2008