Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

  • Aaron E Darling
  • Todd J Treangen
  • Xavier Messeguer
  • Nicole T Perna
Part of the Methods In Molecular Biology™ book series (MIMB, volume 396)


During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns.

Key Words

Microbial evolution sequence alignment comparative genomics genome alignment genome rearrangement lateral transfer Yersinia pestis 



This work was funded in part by National Institutes of Health grant GM62994-02. A.E.D. was supported by NLM grant 5T15LM007359-05. T.J.T. was supported by Spanish Ministry MECD research grant TIN2004-03382-2.


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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Aaron E Darling
    • 1
  • Todd J Treangen
    • 2
  • Xavier Messeguer
    • 3
  • Nicole T Perna
    • 4
  1. 1.Department of Computer SciencUniversity of Wisconsin-MadisonMadison
  2. 2.Department of SoftwareTechnical University of Catalonia-BarcelonaBarcelona
  3. 3.Department of SoftwareTechnical University of Catalonia-Barcelona, Barcelona Supercomputing Center (BSC)Barcelona
  4. 4.Department of Animal Health and Biomedical Sciences Genome CenterUniversity of Wisconsin-MadisonBarcelona

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