QNet: a software package for estimating phylogenetic networks based on quartets

Description

QNet is a software package written in Java which encompasses methods for generating phylogenetic networks from quartet data, as per the method described in [1].

The method takes as input the set of all quartet tree topologies for a given data set, together with a branch length for each topology. These branch lengths must be precomputed by the user.

Included in the package are two simple applications for generating quartet weight data. GWeight utilizes statistical geometry [2] to generate quartet weights. LengthWeighter is a front-end for the Tree-Puzzle software [3] for generating likelihood quartet weights.

Using the quartet data, QNet employs an agglomerative approach to construct a planar split network, that summarises the relations described by the quartets.The resulting networks are output in Nexus format for easy visualization using the SplitsTree software package [4].

The Filterer application may be used to reduce the complexity of networks for ease of visualizing and interpretation of results.

Availability

Download the QNet software (zip 1.63 MB) QNet is copyright (c) Stefan Grünewald, Kristoffer Forslund and Vincent Moulton. The QNet software and its source code are freely available under the GNU General Public License.

Manual

Usage of the program is described in the QNet manual (pdf 80 KB).

References

QNet description and consistency:

  • S.Grunewald, K.Forslund, A.Dress, V. Moulton, QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets, Molecular Biology and Evolution, 24, 2007, 532-538.
  • S.Gruenewald, V.Moulton, A.Spillner, Consistency of the QNet algorithm for generating planar split graphs from weighted quartets, Discrete Applied Mathematics, 157, 2009, 2325-2334.

Statistical geometry:

K.Nieselt-Struwe, A.von Haeseler, Quartet-mapping, a generalization of the likelihood mappimg procedure, Molecular Biology and Evolution, 18, 1204-1219, 2001

Tree-puzzle:

H.A. Schmidt, K. Strimmer, M. Vingron, A. von Haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, 18, 502-504, 2002

Tree-puzzle webpage

SplitsTree:

D.Huson, D.Bryant, Application of phylogenetic networks in evolutionary studies, Molecular Biology and Evolution, 23(2), 254-267, 2006

SplitsTree webpage

Disclaimer

This software is supplied as-is, with no warranty of any kind expressed or implied. We have made every effort to avoid errors in design and execution of this software, but we will not be liable for its use or misuse. The user is solely responsible for the validity and consequences of any results generated.

Support

For technical questions or feature requests, e-mail Kristoffer Forslund at analysis@nyaga.net

Funding

Development of this software was supported in part by EPSRC [Grant EP/D068800/1].

Research Team

Prof. Vincent Moulton, Dr. Andreas Spillner