Difference between revisions of "SEPP"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
| Line 80: | Line 80: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
| + | =Validation= | ||
| + | * Validate 4/5/2018 | ||
Revision as of 21:02, 5 April 2018
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
Validation
- Validate 4/5/2018