Description

FlatNJ (FlatNetJoining) is a program for computing split networks that allow for interior vertices to be labelled while being (almost) planar. The program takes quartet-like data as input (a so-called quadruple system that can be estimated, for example, by the program GenQS --- see below) and generates a split network following an agglomerative approach similar to the one used in methods such as NeighborJoining [5] and NeighborNet [2] (see [1] for details). The resulting network can then be filtered using the approach described in [3] . The actual drawing of the network is generated by applying the method presented in [6] . The network is stored in a file in nexus format. It can be viewed using the SplitsTree software package [4] .

flatnj pictureGenQS (Generator of Quadruple Systems) is a complementary program that computes quadruple systems directly from sequence data, geographic coordinates or split systems. The input to the program should be provided as a block of suitable type within a file in nexus format. In case of multiple sequence alignments also files in fasta format are accepted. For more information on file formats please refer to the manual FlatNJ_manual (PDF, 212Kb)

If you use FlatNJ please cite:

M. Balvočiūtė, M., A. Spillner, and V. Moulton. FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships, Systematic Biology, 2014, 63(3), 383-96.

Availability

FlatNJ together with GenQS can be downloaded from here FlatNJ.zip (704 Kb).

In order to run them on your machine, java must be installed and configured on the system.

For FlatNJ the Gurobi Optimizer is also required (free for academic users). It must be downloaded and installed separately by following the instructions in the manual.

Manual

Detailed installation and usage instructions for FlatNJ and GenQS can be found in the manual which is distributed together with the program and can also be downloaded here FlatNJ_manual.pdf.

Test files

Test files illustrate the different types of input data for GenQS as well as for FlatNJ. They include the files for the datasets used in [1] and are available for download together with the program FlatNJ.zip (704Kb).

Support

For questions and bug reports please e-mail to Monika Balvočiūtė.

References

[1] M. Balvočiūtė, M., A. Spillner, and V. Moulton. FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships, Systematic Biology, 2014, 63(3), 383-96.

[2] D. Bryant and V. Moulton. NeighborNet: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol, 21:255–265, 2004 .

[3] S. Grünewald, K. Forslund, A. Dress, and V. Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Mol Biol Evol, 24:532– 538, 2007.

[4] D. Huson and D. Bryant. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol, 23:254–267, 2006.

[5] N. Saitou and M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4:406–425, 1987.

[6] A. Spillner, B. Nguyen, and V. Moulton. Constructing and drawing regular planar split networks. IEEE/ACM Trans Comput Biol Bioinform, 9:395–407, 2011.

Disclaimer

FlatNJ is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

Research Team

Monika Balvočiūtė, Dr. Andreas Spillner, Prof. Vincent Moulton