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Visualization of multiple alignments, phylogenies and gene family evolution

Nature Methods volume 7, pages S16–S25 (2010)Cite this article

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Abstract

Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.

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Figure 1: Alignment topologies.
Figure 2: Multiple alignment visualization.
Figure 3: Examples of automatically generated summary annotation for an alignment generated by MSA visualization tools.
Figure 4: Euclidean tree layouts.

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Acknowledgements

J.B.P. acknowledges the support of the ENFIN European Network of Excellence (contract LSHG-CT-2005-518254) awarded to G.J.B. Several tools were made available as prereleases to the authors for evaluation purposes, and we thank the individuals and companies who obliged our requests.

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Authors and Affiliations

  1. School of Life Sciences Research, College of Life Sciences, University of Dundee, Dundee, UK

    James B Procter & Geoffrey J Barton

  2. Institute of Genetics and Molecular and Cellular Biology (IGBMC), Strasbourg, France

    Julie Thompson

  3. European Molecular Biology Laboratory, Heidelberg, Germany

    Ivica Letunic

  4. Animal Bioscience Centre, Teagasc, Ireland

    Chris Creevey

  5. Architecture et réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique (CNRS), Strasbourg, France

    Fabrice Jossinet

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  1. James B Procter
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Correspondence to James B Procter.

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Procter, J., Thompson, J., Letunic, I. et al. Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods 7 (Suppl 3), S16–S25 (2010). https://doi.org/10.1038/nmeth.1434

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