Sequence-based techniques for the temporal and geospatial surveillance of microbial pathogens and outbreak analysis.
Multilocus Sequence Typing
Automated suite of tools for the analysis of MLST data from a wide variety of bacterial pathogens.
Development and application of multi-scale methods for typing microbial pathogens, e.g. SNP-typing, k-mer based approaches, multi-locus typing, average nucleotide identity and whole genome comparisons.
Novel Typing Schemes
Annotation and comparison of whole genome sequences for the development of novel SNP- or gene-based typing schemes at different levels of resolution.
Comparison and multi-dimensional clustering of whole genome sequences to infer the genetic basis of clinically relevant phenotypes.
Candidate gene-based and genome-wide approaches to inferring the genetic basis of antibiotic resistance for a wide variety of chemotherapeutics and species.
A wide variety of computational techniques for the comparison of whole genome sequences, within and between species, for the interrogation of specific biological questions.
Evolution & Phylogenetics
Numerous software packages for making inferences about the action of evolutionary forces on gene/protein sequences along with tools for inferring evolutionary relationships among sequences.