Reading assignment:
If you're feeling ambitious you may want to read the MUSCLE papers (and this one) as well as the ProbCons paper.
Also, chapter 6 in the Durbin book gives an excellent overview of multiple sequence alignment. The multiple sequence alignment chapter in Mount is very useful as well.
For very nice reviews of current programs, consult articles by Notredame and by Edgar and Batzoglou. Both are terrific overviews of the field.
If you're feeling ambitious you may want to read the MUSCLE papers (and this one) as well as the ProbCons paper.
Also, chapter 6 in the Durbin book gives an excellent overview of multiple sequence alignment. The multiple sequence alignment chapter in Mount is very useful as well.
For very nice reviews of current programs, consult articles by Notredame and by Edgar and Batzoglou. Both are terrific overviews of the field.