VisRD - Visual Recombination Detection Software package

Description

VisRD is a software package allowing graphical inspection of the phylogenetic content of a sequence alignment, that is primarily intended for detection of recombination and recombination breakpoints. It is a quartet-based method, meaning that analysis is performed on quartets of sequences in the alignment. VisRD can utilize a variety of phylogeny estimation algorithms, of which statistical geometry has been most fully implemented.

Analysis is performed in a window sliding along the sequence alignment, and the results may then be viewed in a variety of ways, most importantly in a so-called highway plot. Other visualisation modes are the occupancy plot and an animated version of a quartet mapping plot. For a full explanation of these options and the underlying theory, please consult either the manual (pdf 187 KB) or the paper (Strimmer et al., 2003) describing the method.

If you use VisRD we would appreciate if you could cite the following paper:

For a short description see:

Availability

The latest version (3.0) is available here (zip 161 KB), this version is standalone.

VisRD is copyright (c) Martin Lott, Kristoffer Forslund and Vincent Moulton. The VisRD software and its source code are freely available here (zip 93 KB)  under the GNU General Public License.

Manual

Usage of the program is described in the VisRD manual (pdf 187 KB). You can also download a test file.

Example Files

Support

For technical questions or feature requests, e-mail Martin Lott.

Acknowledgements

Development of VisRD and research on the underlying methodology was supported by the Swedish Research Council (K.F. and V.M.), The Swedish Foundation for International Cooperation in Research and Education (B.H. and V.M.) and the Deutsche Forschungsgemeinschaft (K.S.).

Version 2.0-2.2 was developed in cooperation with Daniel Huson and collaborators on the SplitsTree4 project. D.H. and V.M. thank ARI (project number HPRI-CT-2001-00153), and the Erasmus exchange program. The VisRD icon is courtesy of the Icon Archive.

References

Application of version 3.0:

  • P. Lemey, M. Lott, D. P. Martin and V. Moulton, Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning, BMC bioinformatics (2009), 126-144

VisRD description:

  • K. Strimmer, K. Forslund, B. Holland and V. Moulton, A novel exploratory method for visual recombination detection, Genome Biology (2003)

Related papers: SplitsTree4

  • A. Dress, D. Huson and V. Moulton, Analyzing and visualizing sequence and distance data using SplitsTree, Discrete Applied Mathematics (1996) 95-109
  • D. H. Huson, SplitsTree: analyzing and visualizing evolutionary data, Bioinformatics (1998), 68-73

Related papers: Statistical Geometry

  • M. Eigen, R. Winkler-Oswatitsch and A. Dress, Statistical geometry in sequence space: A method of quantitative comparative sequence analysis, PNAS (1988), 5913-5917
  • M. Eigen and R. Winkler-Oswatitsch, Statistical Geometry on Sequence Space, Methods in enzymology (1990), 505-530
  • K. Nieselt-Struwe, Graphs in Sequence Spaces: a Review of Statistical Geometry, Biophysical Chemistry (1997), 111-131

Related papers: Quartet-mapping:

  • K. Strimmer and A. von Haeseler, Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment, PNAS (1997), 6815-6819
  • K. Nieselt-Struwe and A. von Haeseler, Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure, Molecular Biology and Evolution (2001), 1204-1219

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.

Research Team 

Dr. Martin LottProf. Vincent Moulton.