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SIM - Alignment Tool for protein sequences
is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences
or within a sequence.
Once the alignment is computed, you can view it using LALNVIEW, a
graphical viewer program for pairwise alignments [references].
Note: You can use the PBIL server to align nucleic acid sequences with a similar tool.
Please enter two sequences. These sequences may either be specified by
accession numbers (AC), e.g. P05130, or by entry names (ID),
e.g. KPC1_DROME, or by pasting
your own sequences into the boxes below.