This section details steps for installing and running SuperFine. We ran
SuperFine on a machine running Linux release 220.127.116.11+desktop10+25.63.
If you experience difficulty installing or running the software, please
contact us at the e-mail address shown on the main
-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
For instructions on obtaining and installing
PAUP*, please visit the PAUP*
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
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.
Downloads for the simulated data from our study are provided below.
Uncompress each using the command "tar -xzf <file>".
Within each resulting directory are four subdirectories, one for
each scaffold density we examined. Inside each scaffold density
directory are the data replicates; for each data replicate, we have
included a file with the source trees and a second file with the
model (i.e. true) tree.
- The paper appeared in Systematic Biology (2012) 61(2):214-227,
doi:10.1093/sysbio/syr092 (first published online September 20, 2011).
for the most recent version of the manuscript.
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