Difference between revisions of "SEPP"
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| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
Revision as of 18:10, 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
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