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hivtrace website  

HIV-TRACE (TRAnsmission Cluster Engine) is an application that identifies potential transmission clusters within a supplied FASTA file.

Environment Modules

Run module spider hivtrace to find out what environment modules are available for this application.

System Variables

  • HPC_HIVTRACE_DIR - installation directory
  • HPC_HIVTRACE_BIN - executable directory

Additional Information

usage: $ hivtrace -h

The hivtrace module also includes the dependency tn93, a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance. This dependency can be used independently with the hivtrace module loaded.

usage: $ tn93 -h


If you publish research that uses hivtrace you have to cite it as follows:

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Mol Biol Evol. 2018 Jul 1;35(7):1812-1819. doi: 10.1093/molbev/msy016.