Hello - A while back someone posted a question about how you could simulate a substitution matrix in an HMM pairwise alignment (relating to the example http://www.biojava.org/docs/bj_in_anger/PairAlign.htm). I gave a pretty poor answer but have since rediscovered the full explanation.
The procedure is outlined on page 118 of Durbin et al, Biological Sequence Analysis and in much more detail in Altschul 1991 (J Mol Biol 219: 555-65) - Mark _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
