Hi, there, The WeightMatrixDemo example at "BioJava In Anger" page (http://bioconf.otago.ac.nz/biojava/weightMatrix.htm?PHPSESSID=0adccafdabe1f2c52b062649c404c50f generates a WeightMatrix from an aligment and uses that matrix to annotate a Sequence with a threshold of 0.1. This program uses the odds ratio. I wonder if BioJava has the capacity to use the log-odds ratio (an additive scoring system) to avoid overflow. So, I guess very slight modification can do the same thing as this program does. Thanks.
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