I led a group of students in research to study genomic sequences from Mycobacteriophages my Junior and Senior years at Brown. The main goal was examine the ~700 published mycobacteriophage genomes using methods independent of sequence alignment. Methods from statistics and information theory frequently come in here. Using metrics based on the occurrence of k-mers (substrings of DNA of length k), we were able to reconstruct phylogenetic trees and search for regions potentially influenced by horizontal gene transfer.
The research resulted in a paper published at F1000Research  and presentations at a few conferences. Below you can find the presentation Chen Ye gave at the 2014 HHMI SEA-PHAGES symposium. Chen is talented with animation and did an incredible job explaining the research in this medium.
 Siranosian B, Perera S, Williams E et al. Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages [version 2; referees: 1 approved]. F1000Research 2015, 4:36 (doi: 10.12688/f1000research.6077.2)
Brown University SEA-PHAGES 2014 Presentation from Chen Ye on Vimeo.