Constructing phylogenetic supernetworks based on simulated annealing

Different partial phylogenetic trees can be derived from different sources of evidence and different methods. One important problem is to summarize these partial phylogenetic trees using a supernetwork. We propose a novel simulated annealing based method called SNSA which uses an optimization function to produce a simple network that still retains a great deal of phylogenetic information. We report the performance of this new method on real and simulated datasets.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► We introduced a new algorithm (SNSA) for constructing supernetworks from partial trees. ► SNSA is based on simulated annealing. ► We compared the results of SNSA with Z-closure and SuperQ algorithms. ► SNSA retains all major splits of the input trees. ► For real and simulated datasets, we find that SNSA produces highly accurate and simple networks.