Multiple alignment of rearranged genomes

The nature of large-scale evolutionary processes that shape genomes over time fundamentally differs from the forces governing local evolution within individual genes. Large-scale events such as horizontal transfer, genome rearrangements, gene duplication, and gene loss obscure the notion of orthology and have demanded new models of evolution. Multiple genome alignment tools must cope with such large-scale changes in addition to local changes such as nucleotide substitution and indels. Using simulated genomes containing both large and small-scale evolutionary changes, we present 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. Our results indicate that in the presence of large-scale rearrangement events, Mauve has superior accuracy. Mauve is available from http: //gel. ahabs.wise.edu/mauve.