Date of Award

Summer 8-12-2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Computer Science

First Advisor

Alexander Zelikovsky

Second Advisor

Yury Khudyakov

Third Advisor

Robert Harrison

Fourth Advisor

Rajshekhar Sunderraman


The genomic diversity of viral quasispecies is a subject of great interest, especially for chronic infections. Characterization of viral diversity can be addressed by high-throughput sequencing technology (454 Life Sciences, Illumina, SOLiD, Ion Torrent, etc.). Standard assembly software was originally designed for single genome assembly and cannot be used to assemble and estimate the frequency of closely related quasispecies sequences.

This work focuses on parsimonious and maximum likelihood models for assembling viral quasispecies and estimating their frequencies from 454 sequencing data. Our methods have been applied to several RNA viruses (HCV, IBV) as well as DNA viruses (HBV), genotyped using 454 Life Sciences amplicon and shotgun methods.