Hello all, 


I have a large DNAStringSet and I am trying to calculate its distance matrix. My DNAStrings are equal width and they are already aligned. 


I have tried using the stringDist() function, but it is very slow for large DNAStringSets. Is there a way to quickly calculate the number of differences between two DNAString instances? 


For example, let's say I have two DNAStrings: "ACAC" and "ACAG". I would like to know if their is a function other than stringDist() that will tell me the distance between them is 1. 


Thanks in advance for any help. 


- Erik 
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