Comparison of sequences. a) Alignment of 5 poxvirus DNA polymerase proteins. In this example, the blue boxes, shown under a sequence, indicate a difference to the top sequence in the MSA. b) Similarity plot calculated with a PAM250 matrix of the MSA shown in (a). The Reference Sequence, Window Size and Step Size can be changed, and the user can zoom into a particular region by using the cursor to draw box on the plot; Re-centre returns the plot to the full size.
Hillary et al. Microbial Informatics and Experimentation 2011 1:2 doi:10.1186/2042-5783-1-2