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\section{Introduction \section{Introduction}  \label{section intro}} intro}  RNA viruses and retroviruses, such as SARS, influenza, hepatitis C, polio, and HIV, use RNA as their genetic material. RNA viruses often evolve because viral RNA polymerases lack the proof-reading ability of DNA polymerases, which rapidly confounds the immune system and medical treatment. 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}. RNA viruses, however, present particular challenges for all sequence based methods of analysis as a result of their high mutation rate and the complex secondary structures of their genomes \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.