The field of epigenetics is rapidly expanding and tools for analyzing the epigenome in the context of evolutionary biology are beginning to become available. I am interested in adapting methods of traditional phylogenetic analysis to epigenetic discoveries. Primarily I am working to understand the evolution of epigenetic plasticity by conservation of underlying DNA motifs that correlate and support epigenetic marks “above the genome”. To accomplish this, I use a number of methods, usually starting with multiple alignments. As next-generation sequencing technology matures, tools such as Clustal Omega, BioStar, and others will enable me to map large numbers of short-reads and derive useful biological insights from massively parallel sequencing efforts.