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HH-suite

Open-source software for sensitive protein sequence searching based on pairwise alignment of Hidden Markov Models (HMMs)

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Get Started

HH-suite provides a comprehensive toolkit for protein homology detection and sequence analysis. Choose your installation method and start searching in minutes.

Installation

Install via conda, Docker, or compile from source

Quickstart Guide

Run your first sequence search in 5 minutes

Core Tools

Explore HHblits, HHsearch, and HHalign

Databases

Download and configure protein databases

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Core Tools

HH-suite includes powerful command-line tools for different protein analysis workflows.

HHblits

Fast iterative sequence database searching

HHsearch

Sensitive protein homology detection

HHalign

Pairwise HMM-HMM alignment

HHmake

Build HMMs from alignments

HHfilter

Filter multiple sequence alignments

HHconsensus

Generate consensus sequences

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Key Features

HMM-HMM Comparisons

Profile-to-profile searches for remote homology detection

SIMD Optimizations

SSE2 and AVX2 support for 2x faster performance

Parallel Computing

MPI and OpenMP support for multi-core processing

Major Databases

Compatible with Uniclust30, BFD, Pfam, and PDB70

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Performance Optimized

HH-suite is designed for high-performance protein sequence analysis:
  • SIMD Instructions: Leverage SSE2, AVX2 for accelerated computation
  • Parallelization: Scale with OpenMP threading and MPI clusters
  • Iterative Search: HHblits performs multiple search iterations efficiently
  • Prefiltering: Fast k-mer-based prefiltering reduces search time
Identify evolutionarily related proteins with very low sequence identity using HHsearch’s sensitive HMM-HMM comparison algorithm.
Generate multiple sequence alignments with HHblits to improve accuracy of structure prediction methods like AlphaFold.
Transfer functional information from known proteins to uncharacterized sequences by detecting distant homologs.
Create custom HMM databases for specialized protein families or organisms using HHmake and database utilities.

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Citation

If you use HH-suite in your research, please cite: 
Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)
HH-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinformatics, 473. doi: 10.1186/s12859-019-3019-7

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Community and Support

GitHub Repository

Report issues and contribute to development

User Guide

Comprehensive wiki with examples and FAQs

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