Heterotachy is a general term to describe positions in a sequence that evolve at 
different rates in different lineages. Kolaczkowski and Thornton (2004. 
Performance of maximum parsimony and likelihood phylogenetics when evolution is 
heterogeneous. Nature 431:980-984.) recently described an intriguing heterotachy 
model that leads to topological bias for likelihood-based methods and parsimony 
methods. In this article, we show that heterotachy can generally be viewed as 
multivariate rates-across-sites variation, which can be described as randomly 
drawing rates (or branch lengths) from a multivariate distribution for each 
branch at each site. Motivated by this idea, we propose a pairwise alpha 
heterotachy adjustment model, which gives us much improved topological 
estimation in the settings by Kolaczkowski and Thornton (2004).