Bioinformatics: sequence and genome analysis. D. W. Mount. Cold Spring Harbor Laboratory Press, New York (2001). http://www.bioinformaticsonline.org Algorithms for molecular biology. R. Shamir. Course lecture notes, Tel Aviv (2001). http://www.math.tau.ac.il/~rshamir/algmb.html Introduction to computational biology. J. Setubal and J. Meidanis. PWS publishing Co, (1997). A general method applicable to the search for similarities in the amino acid sequences of two proteins. S.B. Needleman and C.D. Wunsch. Journal of Molecular Biology 48:443-453 (1970). The multiple sequence alignment problem in biology. H. Carrillo and D. Lipman. SIAM. Journal of Appl. Math. 48:197-209 (1988). Progressive sequence alignment as a prerequisite to correct phylogenetic trees. D.F. Feng and R.F. Doolittle. Journal of Molecular Evolution 25:351-360 (1987). A tutorial on hidden Markov models and selected applications in speech recognition. L.R. Rabiner. Proceedings IEEE, 77:257-286 (1989). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. T.L. Bailey and C. Elkan. Proceedings of the 3rd ISMB conference, 21-29. (1995). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald and J.C. Wootton. Science 262:208-214. (1993). Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. J.D. Thompson, D.G. Higgins and T.J. Gibson. Nucleic Acids Research 22:4673-4680 (1994). The neighbor-joining method: a new method for reconstructing phylognetic trees. N. Saitou and M. Nei. Molecular Biology and Evolution 4:406-425 (1987). T-Coffee: a novel method for fast and accurate multiple sequence alignment. C. Notredame, D.G. Higgins and J. Heringa. Journal of Molecular Biology 302: 205-217 (2000).