JAligner has been ported to C#

[Ahmed Moustafa]

JAligner (http://jaligner.sf.net) is an open source Java implementation
of the Smith-Waterman algorithm with Gotoh's improvement for biological
local pairwise sequence alignment using the affine gap penalty model.

Joannès Vermorel (http://www.vermorel.com) has ported JAligner to C#
"NAligner" (http://jaligner.sf.net/naligner), NAligner is open source
and available for free at (http://sf.net/projects/jaligner).

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