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spruce

Overview

  • spruce is a Python package designed for simple supertree analysis. However, some of the functionality may be of more general interest for work in computational phylogenetics. The code was written to be easy to understand and extend.

Documentation

Citation

  • If you find this software useful, please cite this URL. Here's a sample BibTeX entry:
    @misc{spruce,
          Author = {Rahul Suri and Tandy Warnow},
          Howpublished = {Website},
          Note = {http://www.cs.utexas.edu/~phylo/software/spruce/},
          Title = {spruce},
          Year = {2010}}

Acquiring and Installing

  • 0. Installing python packages.
    • The software packages listed below are Python source distributions. To use them, you must first have Python installed on your system; for details on obtaining and installing Python, please visit the Python home page. We used Python version 2.6.

      To uncompress and inflate each distribution file, run "tar -xzf <package>.tar.gz". To install each package, run "python setup.py install" from inside the uncompressed package directory; this step requires root access to the system.

      If you do not have root access, invoke the setup script as follows: "python setup.py install --prefix=/some/path/on/your/system", where "/some/path/on/your/system" is the path to a directory on your system to which you do have read and write access. If you use the "--prefix" option, you must ensure that the "lib/python2.x/site-packages" subdirectory (where "x" denotes the minor version number of your Python install) of the directory you specify following "--prefix=" is on Python's search path. To add a directory to Python's search path, modify your PYTHONPATH environment variable.

      More instructions on installing Python packages can be found on this Python page.

  • 1. Install the newick_modified package.

  • 2. Install the spruce package.

  • 3. Run an example script.
    • There are several scripts packaged with the download. After installing spruce, they should be available in the bin subdirectory of the path you specified with the --prefix option. Or they'll be in the bin directory of your Python installation, if you installed spruce without the --prefix option. Run any of these scripts with the -h flag for a usage message.

  • 4. A note on PAUP* usage.
    • Some of the functionality in spruce requires that PAUP* be installed and runnable with a system call of the form "paup -n". This includes generating greedy consensuses and calculating parsimony scores. If PAUP* is not installed, other functionality should still be available.

Old Versions

Acknowledgements

Copyright © 2009-2010 Computational Phylogenetics Lab | ACES 3.304 | University of Texas | Austin, TX 78712
Site help/questions/feedback/requests: e-mail Tandy Warnow