Block-wise alignment of nucleotide sequences?

[Andreas Wilm]

Hi,

> Is there a program that performs block-wise alignment of nucleotide
> sequence pairs (i.e. I do not need multiple alignment here)? So far, I
> could only find programs capable of doing that with protein sequences.

What exactly do you mean by "block-wise alignment"?
Maybe Dialign is what you are looking for :
http://bibiserv.techfak.uni-bielefeld.de/dialign/

Regards,
Andreas

-- 

Andreas Wilm
===========================================
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Physikalische Biologie
http://www.biophys.uni-duesseldorf.de/
http://www.biophys.uni-duesseldorf.de/~wilm