Evolutionary Interpretation of Log Odds Scores for alignment Alexei Drummond Department of Computer Science

Evolutionary interpretation of match/mismatch scores xy xy a, b not homologous a, b homologous t xy xy (d=0.1 is roughly 90% similarity) d = average number of changes per site

Jukes Cantor Model All mutations are equally likely –x  y at the same rate for all x, y All nucleotides are equally likely (equal base frequencies: –{0.25, 0.25, 0.25, 0.25} for DNA –{0.05,…,0.05} for Proteins DNA Proteins

Evolutionary interpretation of match/mismatch scores (DNA) xy xy (d=0.1 is roughly 90% similarity) d = average number of changes per site

Evolutionary interpretation of match/mismatch scores (DNA)