Description Usage Format Source Examples
The BLOSUM 62 substitution matrix which may be used for calculating distances. This is the default
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A matrix where element i,j represents how often homologous proteins have element i substituted with element j. Thus, it is a measure of similarity. Positive numbers indicate easy substitution, while negative numbers indicate difficult substitution.
Henikoff, S.; Henikoff, J.G. (1992). "Amino Acid Substitution Matrices from Protein Blocks". PNAS 89 (22): 10915-10919. doi:10.1073/pnas.89.22.10915
1 2 3 4 | data(blosum62)
##Change the normal distance parameters
default.MetricParams <- new("MetricParams", smatrix=blosum62, gapOpen=-10, gapExtension=-0.2)
##Now calls to dist on sequences will use blosum 62 instead
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