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Bioinformatics Advance Access published online on January 19, 2008
Bioinformatics, 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 visualise phylogenetic mosaicism

Moore J.D. 1,* and Allaby R.G. 1

Warwick HRI, University of Warwick, Warwick, CV35 9EF, U.K.

*To whom correspondence should be addressed.Dr. Moore, J.D, E-mail: jonathan.moore{at}warwick.ac.uk, jay.moore{at}warwick.ac.uk


  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 visualises 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 Warwick HRI, University of Warwick, Warwick, CV35 9EF, U.K.

Supplementary information: The decision pathway for phylogenetic analyses is described in Supplementary Fig. 1.

Associate Editor: Prof. Martin Bishop

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

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