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Open Access Methodology article

Drawing explicit phylogenetic networks and their integration into SplitsTree

Tobias H Kloepper* and Daniel H Huson

Author Affiliations

Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen, Germany

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BMC Evolutionary Biology 2008, 8:22  doi:10.1186/1471-2148-8-22

Published: 24 January 2008

Abstract

Background

SplitsTree provides a framework for the calculation of phylogenetic trees and networks. It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface.

Results

In this article, we present solutions to two important problems in the field of phylogenetic networks. The first problem is the visualization of explicit phylogenetic networks. To solve this, we present a modified version of the equal angle algorithm that naturally integrates reticulations into the layout process and thus leads to an appealing visualization of these networks. The second problem is the availability of explicit phylogenetic network methods for the general user. To advance the usage of explicit phylogenetic networks by biologists further, we present an extension to the SplitsTree framework that integrates these networks. By addressing these two problems, SplitsTree is among the first programs that incorporates implicit and explicit network methods together with standard phylogenetic tree methods in a graphical user interface environment.

Conclusion

In this article, we presented an extension of SplitsTree 4 that incorporates explicit phylogenetic networks. The extension provides a set of core classes to handle explicit phylogenetic networks and a visualization of these networks.