One of our Developers gave me the below infromation:
We have 11 well defined Similarity Matrices in Bio.dll. These matrices are constructed from the resource files (.txt). You can find the .txt files under ….Bio\Source\Framework\Bio\SimilarityMatrices\Resources\SimilarityMatrices. We have generic class SimilarityMatrix which does the construction based our StandardSimilarityMatrix enum.
sm = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.Blosum50);
This will get you Blosum50 matrix.
We also support custom matrix by passing your file. Currently, we support ('\t', ' ', ',') delimited matrix files.
SimilarityMatrix sm = new SimilarityMatrix(blosumFilePath);
Please let me know if you need any more clarification.
Fadi Fakhouri on behalf of the MBF Team