Theory

Introduction

• Many viruses are measurably evolving
• This means that if we have sequences sampled over time we can:
  • Root the tree without an outgroup
  • Estimate the rate of evolution
  • Transform the tree into units of time

Strict and relaxed molecular clocks

• Like many organisms, viruses do not evolve at a constant rate
• The evolutionary rate changes, such that the same branch length may not imply the same amount of time
• Methods need to either tolerate or model this rate variation

Approaches to obtaining 'time trees'

• Take an unconstrained tree and transform it to follow a clock
  • phytime
  • chronos
  • Least Squares Dating
• Generate a phylogeny from the sequence data directly, which assumes a molecular clock
  • sUPGMA
  • TREBLE
  • Bayesian inference
    • BEAST
    • MrBayes