My-Closure

MY-CLOSURE is an application for computing supernetworks from partial phylogenetic trees.

MY-CLOSURE: Program for Computing Supernetworks

Description

MY-CLOSURE is an application for computing supernetworks from partial phylogenetic trees.

The program takes as input a text file containing phylogenetic trees in Nexus format [1] (see also our examples) which are not necessarily on the same but overlapping taxa sets. The output is a new Nexus file which contains a collection of weighted splits (i.e bipartitions) on the set of all taxa. This Nexus file can be read by e.g. the SplitsTree4 program [2] which can be used represent the collection of weighted splits in terms of a phylogenetic network. The program is available as a complied JAR file which is platform independent and suitable for running on Windows, Linux and MacOS.

If you use MY-CLOSURE, we would appreciate if you could cite the following paper:
S. Grunewald, K. T. Huber and Q. Wu, 2 Novel Closure Rules for Constructing Phylogenetic Super-networks, Bulletin of Mathematical Biology, 70: 1906-1924, 2008.

Availability

MY-CLOSURE is written in Java, and the most recent version, version 1.0, is complied using J2SE 5.0. MY-CLOSURE is released under the GNU General Public License, the source code is freely available here to modify providing the copyright notice remains intact and due credit is given to the authors in publications.

Usage of the program is described in the MY-CLOSURE manual (4KB,PDF).

MY-CLOSURE is Copyright © 2008 Qiong Wu & Katharina Huber.

Examples

We have also included two test files in Nexus format with the MY-CLOSURE program.

Support

For technical questions or feature requests, e-mail Dr. Katharina Huber.

References

  1. D. R. Maddison, D. L. Swofford & W. P. Maddison, NEXUS: An Extensible File Format for Systematic Information, Systematic Biology 46(4): 590-621, 1997.

  2. D. H. Huson & D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution 23(2): 254-67, 2006.

Disclaimer

This software is supplied as-is, with no warranty of any kind expressed or implied. We have made every effort to avoid errors in design and execution of this software, but we will not be liable for its use or misuse. The user is solely responsible for the validity and consequences of any results generated.

Research Team

Qiong Wu, Dr. Katharina Huber