code: public static PairwiseAlignment create(final int threads, final SubstitutionMatrix substitutionMatrix) {
          return new ParallelBiojavaPairwiseAlignment(Executors.newFixedThreadPool(threads), substitutionMatrix);
      }
docs: Create and return a new pairwise alignment implementation configured with a fixed thread pool and the specified
  substitution matrix.
  
  @param threads number of threads, must be <code>&gt;= 0</code>
  @param substitutionMatrix substitution matrix, must not be null
  @return a new pairwise alignment implementation configured with a fixed thread pool and the specified
  substitution matrix