[Biojava-l] substitution matrices and probability

[mark.schreiber at novartis.com]

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