Phylotree

phylotree is a collection of programs for cophylogeny testing, developed by the Collaboratory in Computing for Bioinformatics and Biomedical Research at the University of Kentucky. phylotree itself is distributed under the GNU General Public License (GPL) version 3, but the distribution includes third-party programs under related licenses; see the full license for more details.

Credits

These programs were developed through government grant funds from the National Institute for Health. Therefore, we request that publications based on these programs cite the following grant.

• NIH Research Project Grant Program (R01) from the Joint DMS/BIO/NIGMS Math/Bio Program (1R01GM086888-01 and 5R01GM086888-02) from August 1st, 2008 to June 30th, 2013. Principal investigator Ruriko Yoshida, co-PIs Christopher L. Schardl and Jerzy W. Jaromczyk.

Some support was provided by:

• KBRIN/INBRE grant NIH 2 P20 RR-16481
• KY NSF EPSCoR Research Infrastructure Initiatives (2008-2013)

Downloads

The current release is 1.0.0.

• Download the phylotree 1.0.0 source code [.tar.gz].
• Browse the phylotree GIT repository.
• Download the sequence alignment data used in our experiments, including both original and processed versions.

Documentation

• Prerequisites for building and running.
• Getting started with phylotree.
• README
• phylo-experiment manual page.
• testphylotree manual page.
• Included experiments and results.
• Copyright and license information.