An Introduction to Multiple Sequence Alignment — and the T-Coffee Shop. Beyond Just Aligning Sequences: How Good can you Make your Alignment, and so What?

I begin the chapter with a discussion of the fundamental principles of multiple-sequence alignment starting with pair-wise dynamic programming, then I move onto significance and similarity statistics, then amino acid scoring matrices, and I end the introduction with multiple-sequence alignment algorithms themselves. Reliability issues, complications, and applications of multiple-sequence alignment are discussed next. The chapter concludes with a description and tutorial about using the T-Coffee multiple-sequence alignment package.