ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
Program is available in version 7
Initialize enviroment ("module add act-7") and run "act".
Documentation is available on http://www.sanger.ac.uk/resources/software/act/.