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SuperFine Materials

Software

  • This section details steps for installing and running SuperFine. We ran SuperFine on a machine running Linux release 2.6.24.6+desktop10+25.63. If you experience difficulty installing or running the software, please contact us at the e-mail address shown on the main SuperFine page.

  • -1. Install PAUP*.
    • SuperFine requires that you first have PAUP* installed and executable via a "paup -n" system command (i.e. the PAUP* binary must be in your Unix executable search path, settable via the PATH environment variable). We used PAUP* version 4.0b10 for Unix; other versions may or may not work with SuperFine.

      For instructions on obtaining and installing PAUP*, please visit the PAUP* home page.

  • 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. Install the dendropy package.

  • 4. Install the reup package.

  • 5. Running SuperFine.
    • Copy the "runReup.py" script from the "bin" subdirectory of the location in which you installed the Python packages to the directory in which you are working. Run the script using the command "python runReup.py -r gmrp <source_trees_file>", where "<source_trees_file>" is the name of a file containing source trees in Newick format.

Data

Manuscript

  • The paper appeared in Systematic Biology (2012) 61(2):214-227, doi:10.1093/sysbio/syr092 (first published online September 20, 2011). Click here for the most recent version of the manuscript.

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