For really long pairwise alignments, you should get Webb Miller's
sim and associated programs. They are available from
groucho.cs.psu.edu
sim is a Smith-Waterman alignment program capable of aligning huge sequences
(there is a published reference of the beta globin regions -- >50Kb!).
The program is really part of a larger suite, and you may wish to
install the other programs to view the alignments. Alternatively,
the output from sim is simple and could easily be adapted for
other output formats.
Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
krobison at nucleus.harvard.edu
