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A Gentle Guide to Multiple Alignment
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/mulali.html

Computational Biology.
http://www.cs.washington.edu/education/courses/527/00wi/

Protein Sequence Alignment and Database Scanning (Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of Oxford)
http://barton.ebi.ac.uk/papers/rev93_1/rev93_1.html