I am currently working on some toy problems to teach myself about sequence alignment. I want to benchmark my efforts against the performance of existing libraries for the JVM (I am developing in Clojure right now). I have learned that org.apache.commons.lang.StringUtils implements Levenshtein distance between two string. However, I will eventually be interested in the problem where different mutations are weighted differently (i.e. insertion may have a higher penalty than substitutions). Can someone point me to a mature Java or Jython library that does this ? I am NOT talking about BLAST or other heuristic methods. For now I want to benchmark against exact methods.