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Bioinformatics Vol. 19 no. 3 2003
Pages 390-395
© 2003 Oxford University Press

SimiTri—visualizing similarity relationships for groups of sequences

John Parkinson * and Mark Blaxter

Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK

Received on May 10, 2002 ; revised on August 14, 2002 ; accepted on September 17, 2002

Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.

Contact: john.parkinson{at}ed.ac.uk

* To whom correspondence should be addressed.


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