Dendroscope3

The dendroscope software is freely available at www.dendroscope.org. It implements the algorithm developed by Huson et al. in their paper entitled Fast Computation of minimum hybridization networks.”In case of interspecific hybrids, the single rooted phylogenetic tree may not be correct as evolutionary history of different genes in hybrids may result in formation of incongruent gene trees.”(Huson et al.2012).They have given an algorithm which takes care of incongruent gene trees and implemented it in the software that they have made- Dendroscope3.The software can be downloaded from their website .They also provide an online licence key for this software which is freely available from their site.
Reference:
Daniel Huson et.al.(2012) Fast Computation of minimum hybridization networks.Bioinformatics 28(2),191-197.