SEPP

Description

sepp website  

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