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jpHMM analysis of South African AC recombinants. (A) Indication of the recombinant breakpoints based on HXB2 numbering. The uncolored regions denote missing information due to the input fragment sequence and the gray regions denote missing information due to uninformative subtype models. (B) Posterior probabilities of the subtypes at each sequence position (original sequence positions) calculated by jpHMM. Color images available online at www.liebertpub.com/aid
