Difference between revisions of "Hivtrace"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Alignment {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPT...") |
(Adding tn93 dependency information) |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
[[Category:Software]][[Category:Biology]][[Category:Alignment]] | [[Category:Software]][[Category:Biology]][[Category:Alignment]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|hivtrace}} |
| − | |{{#vardefine:url| | + | |{{#vardefine:url|https://github.com/veg/hivtrace}} |
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| Line 33: | Line 33: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | usage: hivtrace | + | 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 | ||
| + | |||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 20:00, 24 May 2024
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.
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
Citation
If you publish research that uses hivtrace you have to cite it as follows: