Difference between revisions of "SEPP"
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==System Variables== | ==System Variables== | ||
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_CONF - configuration examples directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 18:11, 12 July 2015
Description
SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
Required Modules
Serial
- sepp
System Variables
- HPC_{{#uppercase:sepp}}_DIR - installation directory
- HPC_{{#uppercase:sepp}}_BIN - executable directory
- HPC_{{#uppercase:sepp}}_CONF - configuration examples directory
Additional Information
The sepp module includes all three components of the SEPP suite - SEPP, TIPP, and UPP - the three methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem..
- SEPP - SATe-enabled phylogenetic placement
- TIPP - Taxonomic identification and phylogenetic profiling
- UPP - Ultra-large alignments using Phylogeny-aware Profiles