SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.

Description

SuperQ is a Java software package which converts a collection of partial input trees into a collection of quartets. From this collection a super network is computed using QNet [3]. The weights for the edges in this super network are calculated by solving an optimization problem. For this purpose the user can choose between different objective functions (linear, quadratic and balanced), which are explained more in detail in [1]. An advantage of SuperQ is that it produces a planar network that makes it easy to grasp the contained information. Furthermore SuperQ provides a method to scale the input trees and to filter the output.

Input to the program can have two different formats, Script or Newick. In the Script format a list of text documents is given. Each text document contains one tree in either Nexus or Newick. If the input is one Newick file, it must contain all partial trees. Please see our test files for examples. The program is available as a compiled JAR file which is platform independent and suitable for running on Windows, Linux and MacOS.

If you use SuperQ we would appreciate if you could cite the following paper:

Grünewald, S., Spillner, A., Bastkowski, S., Boegershausen, A., Moulton, V. (2012). SuperQ: Computing Supernetworks from Quartets.

Availability

SuperQ is written in Java, and the most recent version, version 1.1, is compiled using JDK 1.6. If you are having problems running it please ensure you have Java Runtime Environment (JRE) version 6.0 or above installed. Once you have a suitable JRE installed, download the ​SuperQ  ZIP or TAR.GZ file for one of the supported platforms: <win32>,<win64>, <linux>. A command line version as well as a graphical user interface is provided. Although SuperQ works as a standalone product (JRE excluded), it is recommended that you install the Gurobi Optimizer to get the best results from SuperQ, which is available under a free academic license. The manual, which can be found in the SuperQ package contains more detailed instructions for installing and using SuperQ.

Manual

Usage of the program is described in the SuperQ manual (pdf 140 KB) available to download.

Test files

We have also included a number of test files (zip 4 KB) in Script, Nexus and Newick format as well as the biological data sets used in [1] with the SuperQ program.

Support

For technical questions or feature requests, e-mail Miss Sarah Bastkowski.

References

[1]Grünewald, S., Spillner, A., Bastkowski, S., Boegershausen, A., Moulton, V. (2012). SuperQ: Computing Supernetworks from Quartets.

[2]Grünewald, S., Spillner, A., Forslund, K., Moulton, V. (2008). Constructing Phylogenetic Supernetworks from Quartets, 2008, WABI, 284-295.

[3]Grünewald, S., Forslund, K., Dress, A., Moulton, V. (2006). QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets, Molecular Biology and Evolution, 24(2), 532-538. 

Related papers

[4]Holland, B, Conner, G., Huber, K., Moulton, V. (2007). Imputing Supertrees and Supernetworks from Quartets, Systematic Biology, 56(1), 57-67. 

[5]Huson, D., H., Dezulian, T., Kloepper, T., Steel, M., A. (2004). Phylogenetic Super-Networks from Partial Trees, Transactions on Computational Biology and Bioinformatics, 1(4), 151-158.

[6]Grünewald, S., Huber, K., Wu, Q. (2007). Phylogenetic networks form partial trees, arxiv.org/abs/0709.0283

References

Huson, D. H., Rupp, R., Scornavacca, C. (2010). Phylogenetic Networks, Cambridge University Press.

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.

SuperQ is released under the GNU General Public License 3.0, 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. 

Research Team

Dr. Stefan Grünewald, Dr. Andreas SpillnerMiss Sarah BastkowskiProf. Vincent Moulton