For: Comparing sequences without using alignment scores :
Application to HIV/SIV subtypings.

G. Didier, L. Debomy, M. Pupin, M. Zhang, A. Grossmann, C. Devauchelle and I. Laprevotte

Under submission

 For: HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation; « retroviral signatures» of overrepeated oligonucleotides, and a  probable important role of scrambled stepwise duplications/deletions in molecular evolution

Ivan Laprevotte, Maude Pupin, Eivind Coward, Gilles Didier, Christophe Terzian, Claudine Devauchelle, and Alain Hénaut

Mol. Biol. Evol. 18(7):1231-1245. 2001