So what we want to study is the minor variant changes that occur as a result of culturing HSV. As in, there is more than one variant of HSV in a sample and the percentage of each variant will change if one variant is more fit in a new environment. We have sequencing data from uncultured swabs and data after one passage on Vero cells. Right now I have the minor variants of each sample on its own. This is done by assembling a consensus genome for that sample and then using a SNP caller (VarScan) to look at these minor variants. It makes sense to present some of the results as "this variant was not present in uncultured but is present in cultured." I want to compare the consensus genome too. To show most of the population in this sample had this nucleotide but it was different in this population. How can do this? I could align with clustal omega but I'm not sure if using genomes would overwhelm it. I have only ever used one gene from a few organisms in clustal omega. Any suggestions?