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Accurately estimating the structure of highly diverse viral populations is a challenging task. There are two main impediments to globally reconstructing a population. The first is the presence of sequencing errors in reads. Judiciously differentiating these errors from actual rare variants must be properly handled or the global structure may be ill-defined. Secondly, long conserved regions in the viral genome extend beyond what modern sequencers are capable of producing. As a result, the actualdoi:10.1109/iccabs.2013.6629224 dblp:conf/iccabs/MancusoAZSM13 fatcat:wqvrsc64gvbwbhu2i7up4vnt2i