hivtrace¶

Description¶

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.

Environment Variables¶

HPC_HIVTRACE_DIR - installation directory
HPC_HIVTRACE_BIN - executable directory

Additional Usage Information¶

To view the hivtrace help message, run the following command:

$ 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:

$ tn93 -h

Citation¶

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. http://doi.org/10.1093/molbev/msy016

Categories¶

biology,alignment