All domains of modern biology are increasingly dependent on computation and this dependence on algorithms is most readily apparent in the disciplines that utilise genetic data.

One of the areas most impacted by the rapid rate of advances in high throughput DNA sequencing has been the study of microbial ecology. Sequencing of the microbial marker gene 16S rRNA is typically used to survey the species composition of microbial communities.

The analysis of molecular sequence divergence is central to phylogenetic reconstruction and to dissecting the relative contributions of mutation and natural selection. Phylogenetic reconstruction is the estimation of the relationships amongst a group of sequences.

Much of our understanding of how evolution has operated stems from analyses of genetic differences between species. One feature of our work has been application of very parameter rich models for modelling DNA sequence evolution. Using these models raises numerous challenges that are both statistical and computational.