June 2010 | Volume 5 | Issue 6 | e11147 | Aaron E. Darling, Bob Mau, Nicole T. Perna
The paper introduces a new method called progressiveMauve for aligning multiple genomes that have undergone rearrangements due to recombination and segmental gain and loss. The method uses a novel objective function called the sum-of-pairs breakpoint score to accurately detect rearrangement breakpoints, even when genomes have unequal gene content. It also employs a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences. The authors demonstrate the accuracy of the method through simulations and apply it to a set of 23 genomes from the genera *Escherichia*, *Shigella*, and *Salmonella*. The analysis reveals substantial population-level variability driven by segmental gain and loss, particularly in intergenic regions, suggesting regulatory divergence in the Enterobacteriaceae. The software is freely available as open-source C++ code.The paper introduces a new method called progressiveMauve for aligning multiple genomes that have undergone rearrangements due to recombination and segmental gain and loss. The method uses a novel objective function called the sum-of-pairs breakpoint score to accurately detect rearrangement breakpoints, even when genomes have unequal gene content. It also employs a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences. The authors demonstrate the accuracy of the method through simulations and apply it to a set of 23 genomes from the genera *Escherichia*, *Shigella*, and *Salmonella*. The analysis reveals substantial population-level variability driven by segmental gain and loss, particularly in intergenic regions, suggesting regulatory divergence in the Enterobacteriaceae. The software is freely available as open-source C++ code.