Difference between revisions of "CLUMPP"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EXE - examples directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_CONF - paramfile directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:10, 6 December 2019
Description
CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment.
Required Modules
Serial
- clumpp
System Variables
- HPC_CLUMPP_DIR - installation directory
- HPC_CLUMPP_BIN - executable directory
- HPC_CLUMPP_DOC - documentation directory
- HPC_CLUMPP_EXE - examples directory
- HPC_CLUMPP_CONF - paramfile directory
Additional Information
You must have configuration files to be able to run this software. The example configuration file can be copied using the following command:
cp $HPC_CLUMPP_CONF/* .
Citation
If you publish research that uses clumpp you have to cite it as follows:
Bioinformatics 23: 1801-1806 (2007)