Thomas Leitner

wavess 1.2 simulates within-host virus sequences with an HLA-aware CTL response and variable recombination rate to improve accuracy in immune-dominated regions.

Hypermut 3 detects hypermutation patterns in sequences, handling multistate characters and gaps, and is available as a web and command-line tool.

The paper develops a simulation tool to assess how contact tracing affects phylogenetic inferences from molecular epidemiology data.

This paper develops a deep learning method for real-time HIV outbreak detection using genomic data, achieving high specificity and sensitivity in identifying outbreaks.