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Bioinformatics Advance Access originally published online on June 9, 2006
Bioinformatics 2006 22(17):2162-2163; 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

SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides

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

1 School of Biological Sciences Sydney, Australia
2 Sydney University Biological Informatics and Technology Centre 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.

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

Contact: lars.jermiin{at}usyd.edu.au

Received on March 20, 2006; accepted on May 26, 2006

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