Mauve: multiple alignment of conserved genomic sequence with rearrangements.

@article{Darling2004MauveMA,
  title={Mauve: multiple alignment of conserved genomic sequence with rearrangements.},
  author={Aaron E. Darling and Bob Mau and Frederick R. Blattner and Nicole T. Perna},
  journal={Genome research},
  year={2004},
  volume={14 7},
  pages={
          1394-403
        }
}
As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under… Expand
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An alignment quality comparison of Mauve, a multiple genome aligner that considers large-scale evolutionary events, to alignments generated by other state-of-the-art genome alignment systems indicates that in the presence of large- scale rearrangement events, Mauve has superior accuracy. Expand
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TLDR
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