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This repository includes code for SEPP, TIPP, UPP, HIPPI. The three methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem.

Each of these related tools has its own README file.

  • SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

  • TIPP stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data.

  • UPP stands for "Ultra-large alignments using Phylogeny-aware Profiles", and addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences.

  • HIPPI stands for "Highly Accurate Protein Family Classification with Ensembles of HMMs", and addresses the problem of classifying query sequences to protein families.

Bugs and Errors

SEPP, TIPP, UPP, HIPPI are under active research development at UIUC by the Warnow Lab (and especially with her PhD student Mike Nute and former students Siavash Mirarab and Nam-phuong Nguyen). Please report any errors to Siavash Mirarab (, Nam Nguyen (, or Mike Nute (

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