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\section{Introduction} \label{section intro}  RNA viruses and retroviruses, such as SARS, influenza, hepatitis C, polio, and HIV, use RNA as their genetic material. RNA polymerasesused to replicate these genomes  lack the proof-reading ability of DNA polymerases, which results in a high mutation rate in these viruses. The RNA genomes. This  rapid rate of genome evolution can be advatageous for the virus as it can confound the immune system and medical treatment. The rapid rate of sequence evolution also confounds efforts to tease apart the evolutionary signal of adaptation (e.g. drug resistance) from neutral evolutionary processes such as genetic drift. Phylogenetic and molecular evolutionary analyses of viral genes and genomes have become standard tools for investigating RNA virus evolution at a molecular level \citep{Norstrom2012}. However, the high mutation rate and the complex secondary structures of RNA viruses genomes often compromise sequence based methods of analysis \citep{Simmonds1999, Damgaard2004, Watts2009, Cuevas2012}. Adaptation by the virus to a host or to a drug treatment further complicates sequence analysis because compensatory mutations that offset structural defects and other pleiotropic costs of adaptive alleles often arise and sweep to fixation in viral populations \citep{Knies2008}. Thus there is a critical need for analytical methods that identify regions of the viral genome that have changed over time and are robust to these complications by making minimal assumptions about how the virus should evolve.