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 [4]. 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 [2]. 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.

If you use SuperQ please cite:

S. Grünewald, A. Spillner, S. Bastkowski, A. Boegershausen, and V. Moulton. SuperQ: Computing Supernetworks from Quartets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(1), 151-160, 2013.

Availability

The current version of SuperQ is now available as part of the SPECTRE suite [1]. For more information on how to download, install and use the program refer to the SPECTRE web page.

References

[1] S. Bastkowski, D. Mapleson, A. Spillner, T. Wu, M. Balvočiūtė, and Vincent~Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. 2017. Submitted.

[2] S. Grünewald, A. Spillner, S. Bastkowski, A. Boegershausen, and V. Moulton. SuperQ: Computing Supernetworks from Quartets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(1), 151-160, 2013.

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

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

Related papers

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

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

[7] S. Grünewald, K. Huber and Q. Wu. Phylogenetic networks form partial trees, arxiv.org/abs/0709.0283. 

 

Research Team

Dr. Stefan Grünewald, Dr. Andreas Spillner, Dr. Sarah Bastkowski, Prof. Vincent Moulton