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Bioinformatics Advance Access published online on August 18, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn434
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex

Chaka Tang 1, Josephine F. Reyes 1,2,*, Fabio Luciani 1, Andrew R. Francis 3 and Mark M. Tanaka 1,2,*

1School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
2Evolution & Ecology Research Centre, University of New South Wales, NSW 2052, Australia
3School of Computing and Mathematics, University of Western Sydney, NSW 1797, Australia

*To whom correspondence should be addressed. Josephine F. Reyes, E-mail: j.reyes{at}student.unsw.edu.au. Mark M. Tanaka, E-mail: m.tanaka{at}unsw.edu.au


  Abstract

spolTools is a collection of online programs designed to manipulate and analyze spoligotype data sets of the Mycobacterium tuberculosis complex. These tools are integrated into a repository currently containing 1179 spoligotypes and 6278 isolates across 30 data sets. Users can search this database to export for external use or to pass on to the integrated tools. These tools include the computation of basic population genetic quantities, the visualization of clusters of spoligotype patterns based on an estimated evolutionary history and a procedure to predict emerging strains – genotypes associated with elevated transmission.

Availability: Availability: Database, programs and documentation may be accessed online at http://www.emi.unsw.edu.au/spolTools.

Contact: j.reyes{at}student.unsw.edu.au, m.tanaka{at}unsw.edu.au

Associate Editor: Prof. Martin Bishop

Received on May 27, 2008; revised on August 14, 2008; accepted on August 14, 2008

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