Hivtrace

Description

[REPLACE REPLACE website]  

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

Environment Modules

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

System Variables

• HPC_REPLACE_DIR - installation directory
• HPC_REPLACE_BIN - executable directory

Additional Information

usage: hivtrace [-h] -i INPUT -a AMBIGUITIES -r REFERENCE -t THRESHOLD -m

               MINOVERLAP -g FRACTION [-u CURATE] [-f FILTER]
               [-s STRIP_DRAMS] [-c] [--do-not-store-intermediate]
               [--skip-alignment] [--attributes-file ATTRIBUTES_FILE]
               [--log LOG] [-o OUTPUT] [-p PRIOR]

Citation

If you publish research that uses REPLACE 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.