Difference between revisions of "SEPP"

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* Validate 4/5/2018

Revision as of 21:02, 5 April 2018


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


  • 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


  • Validate 4/5/2018