Detecting the homology of DNA-sequences based on the variety of optimal   alignments: a case study
  We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four genes. 
Erik Hirmo and J\"uri Lember and Heinrich Matzinger
stat.AP q-bio.QM