The package Cassis implements methods for precise detection of genomic rearrangement breakpoints.

As far as we know, the current methods for detecting breakpoints (Mauve, GRIMM-synteny, Magic, etc.) are in fact procedures for detecting synteny blocks. The breakpoint regions are provided as a byproduct, simply by identifying intervals which are not covered by the synteny blocks. The method implemented in Cassis aims to go one step further and to extend the synteny blocks by focusing on the breakpoints themselves.