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Bioinformatics Advance Access published online on June 9, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl283
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 20, 2006
Accepted May 26, 2006

Applications note

SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides

Joshua W. K. Ho 1, Cameron E. Adams 2, Jie Bin Lew 2, Timothy J. Matthews 2, Chiu Chin Ng 2, Arash Shahabi-Sirjani 2, Leng Hong Tan 2, Yu Zhao 2, Simon Easteal 3, Susan R. Wilson 4, and Lars S. Jermiin 1 *

1 School of Biological Sciences, University of Sydney, Sydney, Australia; Sydney University Biological Informatics and Technology Centre, Sydney, Australia
2 School of Biological Sciences, University of Sydney, Sydney, Australia
3 John Curtin School of Medical Research, Australian National University, Canberra, Australia
4 Mathematical Sciences Institute, Australian National University, Canberra, Australia

* To whom correspondence should be addressed.
Lars S. Jermiin, E-mail: lars.jermiin{at}usyd.edu.au


  Abstract

Summary: Most phylogenetic methods assume that the sequences evolved under homogeneous, stationary, and reversible conditions. Compositional heterogeneity in data intended for studies of phylogeny suggests that the data did not evolve under these conditions. SeqVis, a Java application for analysis of nucleotide content, reads sequence alignments in several formats and plots the nucleotide content in a tetrahedron. Once plotted, outliers can be identified, thus allowing for decisions on the applicability of the data for phylogenetic analysis.

Availability: http://www.bio.usyd.edu.au/jermiin/programs.htm.

Associate Editor: Keith A Crandall
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