Bacterial genomics and computational group theory : the BioGAP package for GAP

Bacterial genomes can be modelled as permutations of conserved regions. These regions are sequences of nucleotides that are identified for a set of bacterial genomes through sequence alignment, and are presumed to be preserved through the underlying process, whether through chance or selection. Once a correspondence is established between genomes and permutations, the problem of determining the evolutionary distance between genomes (in order to construct phylogenetic trees) can be tackled by use of group-theoretical tools. Here we review some of the resulting problems in computational group theory and describe BioGAP, a computer algebra package for genome rearrangement calculations, implemented in GAP.