SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees.
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 . 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 . 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.
 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.
 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.
 B. Holland, G. Conner, K. Huber, and V. Moulton. Imputing Supertrees and Supernetworks from Quartets, Systematic Biology, 56(1), 57-67, 2007.
 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.
 S. Grünewald, K. Huber and Q. Wu. Phylogenetic networks form partial trees, arxiv.org/abs/0709.0283.