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Baobab tree

The TreeMos application provides a high-thoughput phylogenomic approach to search for and visualise phylogenetic mosaicism.

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.

TreeMos is designed to run on Mac OS X, Windows and Linux. The Intel Mac OS X 10.4 and 10.5 installer may also work on Power PC Macs with finkLink opens in a new window installed. Contact us if you would like to run TreeMos on other platforms.

  • To install TreeMos 1.0e for Intel Mac OS X 10.4 and 10.5 in your Applications folder.
  • To install TreeMos for Windows.
  • To install TreeMos for Linux.

This program is not available to download at this time.

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Please cite the following paper if you use TreeMos results in a publication:

Moore, J.D., Allaby R.G. (2008) TreeMos: a high-throughput phylogenomic approach to find and visualise phylogenetic mosaicism. Bioinformatics 24(5):717-718.

The TreeMos software uses the algorithm described in Allaby, R.G. & Woodwark, M. (2007) Evolutionary Bioinformatics 3:155-168.

Please note that this is the first full release of this software, and we have not been able to test every possible combination of data sets, parameters, operating systems, and computing platforms. Please take this into account if using this software for publication purposes.



The baobab tree logo is from a photograph of an original mosaic by Brett Campbell and is used with the kind permission of the artist.

Development of TreeMos was part-funded by BBSRCLink opens in a new window.