Richard Neher
Microbial Evolution
University of Basel
Group Webpages:

What do we do?

Our goal is to understand how evolution works at the molecular level and how organisms adapt to changing conditions through random mutations and recombination. Pathogens provide excellent model systems for studying these processes. We apply modern sequencing techniques to decipher the genome of thousands of HIV particles and develop new algorithms to elucidate the interactions between HIV and the immune system. We have developed a method that can predict the evolution of influenza viruses based on their phylogenetic tree ( Such predictions can help to ensure that the seasonal influenza vaccine matches the viruses in circulation.

Reconstructed phylogenetic tree

Reconstructed phylogenetic tree and geographical spread of influenza viruses (

Main publications 2017

  • Puller V et al. Estimating time of HIV-1 infection from next-generation sequence diversity. PLOS Comput Biol. 13 e1005775. 10.1371/journal.pcbi.1005775
  • Zanini F et al. In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evol. 2017 Mar 2;3(1):vex003. doi: 10.1093/ve/vex003
  • Ding W et al. panX: pan-genome analysis and exploration. Nucleic Acids Res. 10.1093/nar/gkx977

Our main research topic: