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Bioinformatics Advance Access originally published online on January 19, 2008
Bioinformatics 2008 24(5):717-718; doi:10.1093/bioinformatics/btn027
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism

J. D. Moore * and R. G. Allaby

Warwick HRI, University of Warwick, Warwick, CV35 9EF, UK

*To whom correspondence should be addressed.


  Abstract

Summary: TreeMos is a novel high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences. TreeMos uses a sliding window and local alignment algorithm to identify the nearest neighbour of each sequence segment, and visualizes instances of sequence segments whose nearest neighbour is anomalous to that identified using the global alignment. Data sets can include whole genome sequences allowing phylogenomic analyses in which mosaicism may be attributed to recombination between any two points in the genome. TreeMos can be run from the command line, or within a web browser allowing the relationships between taxa to be explored by drill-through.

Availability: http://www2.warwick.ac.uk/fac/sci/whri/research/archaeobotany

Contact: jonathan.moore{at}warwick.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on September 6, 2007; revised on January 16, 2008; accepted on January 16, 2008

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