* Computes a pairwise similarity matrix for the given sequence regions using
* the configured score model. If the score model is a similarity model, then
* it computes the result directly. If it is a distance model, then use it to
* Computes a pairwise similarity matrix for the given sequence regions using
* the configured score model. If the score model is a similarity model, then
* it computes the result directly. If it is a distance model, then use it to