As RNA viruses mutate and adapt to environmental changes, often developing resistance to anti-viral vaccines and drugs, they form an ensemble of viral strains--a viral quasispecies. While high-throughput sequencing (HTS) has enabled in-depth studies of viral quasispecies, sequencing errors and limited read lengths render the problem of reconstructing the strains and estimating their spectrum challenging. Inference of viral quasispecies is difficult due to generally non-uniform frequencies of the strains, and is further exacerbated when the genetic distances between the strains are small.