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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. RNAviruses often evolve because viral RNA  polymerases lack the proof-reading ability of DNA polymerases, which rapidly confounds results in a high mutation rate in these RNA genomes. The 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}. RNA viruses, however, present particular challenges for all sequence based methods of analysis as a result of their However, the  high mutation rate and the complex secondary structures of their 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. This need for new annotation free analytical tools has been amplified by the wealth of new viral sequence data made possible by recent advances in sequencing technology \citep{Jabara2011}. Increasingly, populations of thousands of viruses are sampled and sequenced from an infected individual, this approach captures a snapshot of the viral genetic variation within an individual. A couple studies have combined this approach with traditional passage experiments or sampling during the course of an infection \citep{Eriksson2008, Kuroda2010, Leitner1993, Wright2010}. This powerful approach reveals how genomically a population of viruses responds to evolutionary pressure. With the ever-decreasing cost of sequencing, these studies are expected to become commonplace.