Allan Wilson Centre for Molecular Ecology and Evolution



Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allowing the user to interactively analyze the resulting collection using tools such as Lento-plots and median networks.

The package was developed jointly by Mike Hendy, Katharina T. Huber, Michael Langton (who also wrote the original source code which has been extended by Tim White), Vincent Moulton, and David Penny.

This documentation was written by Katharina T. Huber with contributions from Michael Langton, Mike Hendy, and Tim White.

Contents

Spectronet is described in the following paper:

Spectronet: A package for computing spectra and median networks, K. T. Huber, M. Langton, D. Penny, V. Moulton and M. Hendy, Applied Bioinformatics 1(3), (2002) 159-161.

Download a preprint of this paper as:

Requirements and Installation
Register for Software Updates
Download the package
Theoretical Background
NEXUS File Format
Program Features and Operations
Examples
Disclaimer
Links to Related Programs
References

Requirements and Installation


The Spectronet package is written in C++ and was initially developed on a dual Pentium III 650 MHz with 256MB RAM, running Windows 2000. It has been tested successfully on a 486DX4/100 with 32MB RAM and Windows 95, and runs under both Windows 95 and Windows NT 4.0 and later versions for each of these. It requires less than 1 Mb in diskspace and it can handle up to 128 taxa represented by sequences of length of up to 50,000 nucleotides, depending on which of the two options is chosen to generate splits.

Installing Spectronet requires the WinZip compression program. A free trial version is available at http://www.winzip.com/, as well as numerous other shareware download sites.

To install Spectronet, go to the directory where you downloaded the Spectronet.zip file and double-click the file to open it in WinZip. Now find the setup.exe file in the listing presented and double-click that to run it. WinZip will ask you if it should extract the files into a temporary directory; click OK. From this point on you will be guided through the installation process by a succession of dialog boxes. If you accept the defaults provided, Spectronet will be installed in the directory C:\Program Files\Spectronet, and shortcuts to the program will be placed on the Start Menu under Programs, and on the desktop. The .NEX and .NXS file extensions will be associated with Spectronet the first time you run the program, so that double-clicking a file with one of these extensions opens it in Spectronet.

WinZip will most likely still be running after the installation is complete. Click OK in the message window and then exit the application.

Spectronet does not require, or install, extra libraries or DLLs.

Examples

Three example data sets come with the package.
  • matK.nxs, a plant data set (more precisely the matK region of the chloroplast of various buttercups) which was studied in Huber et.al. 2001(a),
  • HBV-C-8.nxs, a viral DNA data set. The taxa are labeled by their GenBank accession numbers.
  • mt10.nxs, a mammalian mtDNA data set.

Disclaimer

All people involved in the development of the package have tried their best to keep the number of bugs to a minimum. However no matter how hard one tries, there will always be some bugs left and so no warranty can be given on the results produced by the various components of the package.

Links to Related Phylogeny Programs

Charleston, M. (1996): Spectrum,

Huson, D. (1998): SplitsTree,

Jakobsen I.B. and Easteal S. (1996): Reticulate,

Makarenkov, V. (2001): T-REX,

Roehl, A. (1999): Network.

For a good selection to other phylogeny programs, see Joe Felsenstein's lab web page.

References

Bandelt, H.-J. (1994) Phylogenetic networks. Verhandl. Naturwiss. Vereins Hamburg (NF) 34:51-71.

Bandelt, H.-J., Forster, P., Sykes, B.C., and Richards, M.B. (1995) Mitochondrial portraits of human population using median networks. Genetics, 141, 743--753.

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17: 368-376.

Hendy, M.D., and Penny, D. (1989) A framework for the quantitative study of evolutionary trees. Syst.Zool., 38, 297-309.

Hendy, M.D., and Penny, D. (1993). Spectral analysis of phylogenetic data, J. Classif., 10, 5-24.

Hendy, M.D., Penny, D., and Steel, M.A. (1994) Discrete Fourier analysis for evolutionary trees, Proc. Nat. Acad. Sci. (USA), 91, 3339-3343.

Huber, K.T., Moulton, V., Lockhart, P. and Dress, A. (2001)(a) Pruned median networks: a technique for reducing the complexity of median networks. Molecular Phylogenetics and Evolution 19:302-310.

Huber, K.T., Watson E.E., Hendy, M. (2001)(b) An algorithm for constructing local regions in a phylogentic network. Molecular Phylogenetics and Evolution, 19:1-8.

Jakobsen I.B., and Easteal S. (1996) A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences, CABIOS, 12, 291-295.

Jukes T., and Cantor, C. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism (Munro, H. ed) pp. 21-132, New York: Academic Press

Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 17, 111-120.

Kimura, M. (1981) Estimation of evolutionary sequences between homologous nucleotide sequences, Proc. Nat. Acad. Sci. (USA), 78, 454-458.

Lento, G.M., Hickson, R.E., Chambers G.K., and Penny, D. (1995) Use of spectral analysis to test hypotheses on the origin of pinninpeds. . Mol. Biol. Evol., 12, 28-52.

Saillard J., Forster P., Lynnerup N., Bandelt H.-J., Nørby S. (2000) mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet 67:718-726.

Steel, M.A., Hendy, M.D., and Penny, D. (1998) Reconstructing phylogenies from nucleotide probabilities - a survey and some new results. Discr. Appl. Math., 88, 367-396.

Watson E., Forster P., Richards M. B., Bandelt H.-J. (1997) Mitochondrial footprints of human expansions in Africa. American Journal of Human Genetics 61:691-704.

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