Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions
Distance-based phylogenetic reconstruction methods use evolutionary distances between species in order to reconstruct the phylogenetic tree spanning them. There are many different methods for estimating distances from sequence data. These methods assume different substitution models and have different statistical properties. Since the true substitution model is typically unknown, it is important to consider the effect of model misspecification on the performance of a distance estimation method.
phylogenetic reconstructions substitution models additive substitution rate functions