PhippsNetwork

PhippsNetwork is a Java implementation of Algorithm A2 from the paper "Optimizing phylogenetic networks for circular split systems" by Paul Phipps and Sergey Bereg, published in TCBB in 2012.

Description:

This Java application uses the circular splits generated by SplitTree4's implementation of Neighbor-Net to construct a planar network with few faces. In this resulting network, the lengths of the shortest paths between taxa are the same as those produced by the Equal Angle (Splits Network) algorithm. Typically, Algorithm A2's networks contain far fewer faces than are contained in Splits Networks.
Usage:
java phippsNetwork/Main [-r] [-w] [-u] input_file output_file
(or just run PhippsNetwork.bat)
input_file:
a detailed .nex file (generated by SplitsTree4) that contains circular split information. To ensure that the .nex file has split information, open the file in SplitsTree4 (available here). By default, SplitsTree4 will use Neighbor-Net and EqualAngle methods to produce a network. Save a copy, and use that .nex file name as input to PhippsNetwork. (Note: PhippsNetwork will draw the network with edge lengths of 1 in SplitsTree4, if the option 'Use Weights' is unchecked in the Splits->Method tab of the Network/Draw Dialog Window, and option -w is not used.)
output_file:
a detailed .nex file (readable by SplitsTree4) that contains a network and its vertex coordinate information, for drawing it in SplitsTree4.
Options:
-r Reduce vertices of degree 2. (alters edge lengths, but not weights)
-u (Unweighted) Force the network to draw all edges with length 1.
-w (Weighted) Force the network to draw edge lengths equal to split weights.
Examples:
java phippsNetwork/Main input.nex output.nex
java phippsNetwork/Main -r input.nex output.nex
java phippsNetwork/Main -u input.nex output.nex
java phippsNetwork/Main -w -r input.nex output.nex

Instructions:

  1. Download the Zip file (right click, and "Save link as...") from this link: [DOWNLOAD PhippsNetwork_1_01.zip]
  2. Unzip the file.
  3. For Windows user, run the batch file PhippsNetwork.bat. By default, the input file is input.nex. If the program produces the output file output.nex, then everything should be working.
  4. To run the program on your own .nex file, you have two options:
    1. Edit the batch file PhippsNetwork.bat, then run it.
    2. Run the class file directly with parameters for input and output file names, according to the usage described above.

Disclaimer:

This program may contain bugs. We do not accept responsibility for any problems that arise from use of this software. Use entirely at your own risk.

This software is not affiliated with SplitsTree4 or SplitsTree.org.

References:

  1. D. Bryant and V. Moulton. 2004. "Neighbor-Net: an agglomerative algorithm for the construction of planar phylogenetic networks," Mol. Biol. Evol. 21:255265.
  2. A. W.M. Dress, D. H. Huson, "Constructing Splits Graphs," IEEE/ACM Transactions on Computational Biology and Bioinformatics, pp. 109-115, July-September, 2004.
  3. SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Paper: D.H. Huson and D. Bryant "Application of Phylogenetic Networks in Evolutionary Studies," Molecular Biology and Evolution 23(2):254-267, 2006.

© 2010 Paul Phipps
[email protected]
PhD student, Computer Science Department
The University of Texas at Dallas
800 West Campbell Road
Richardson, TX 75080, USA

Email me with any comments or concerns. If you like this program, I'd love to hear from you.