The N-local-decoding method has shown its satisfactory
applications in HIV/SIV subtyping. The deduced classifications are in
good agreement with our best taxonomic knowledge, even for non-coding
LTR regions that are not tractable by regular alignment methods due to
frequent duplications/insertions/deletions. However, its application is
not limited in HIV/SIV subtyping. In general, the advantages of this
1) It generates sequence dissimilarity matrices without requiring sequence alignments.
2) It has only one user-specified parameter (N: the order of the site neighborhoods).
3) It is fast.
Thus the N-local-decoding method provides a promising
approach to the rapid construction of trees without a time-consuming
step of aligning sequences.