Installation

Prerequisites

Before installing HH-suite, verify your system meets the requirements:

Check 64-bit System

uname -a | grep x86_64

You should see x86_64 in the output.

Check CPU Instruction Set

On Linux:

cat /proc/cpuinfo | grep sse2

On macOS:

sysctl -a | grep machdep.cpu.features | grep SSE2

If you have AVX2 support, HH-suite will run approximately 2x faster than with SSE2.

Installation Methods

Conda (Recommended)
Docker
Precompiled Binaries
Compile from Source

The easiest way to install HH-suite is using conda or mamba:

conda install -c conda-forge -c bioconda hhsuite

This installs HH-suite and all its dependencies in a single command. Perfect for getting started quickly.

Verify Installation

hhblits -h

Using Mamba (Faster)

If you have mamba installed, you can use it for faster dependency resolution:

mamba install -c conda-forge -c bioconda hhsuite

Run HH-suite in a Docker container without installing it locally:

docker pull soedinglab/hh-suite

Run HHblits with Docker

docker run -v $(pwd):/data soedinglab/hh-suite \
  hhblits -i /data/query.fasta -d /data/database -o /data/results.hhr

The -v $(pwd):/data flag mounts your current directory to /data inside the container, allowing you to access local files.

Interactive Docker Session

docker run -it -v $(pwd):/data soedinglab/hh-suite /bin/bash

Download statically compiled binaries for Linux systems. Choose between SSE2 and AVX2 builds:

SSE2 Build (Compatible with older CPUs)

wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-SSE2-Linux.tar.gz
tar xvfz hhsuite-3.3.0-SSE2-Linux.tar.gz
export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

AVX2 Build (Recommended for modern CPUs)

wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz
tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz
export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

Add the export command to your ~/.bashrc or ~/.zshrc to make the PATH change permanent:

echo 'export PATH="/path/to/hhsuite/bin:/path/to/hhsuite/scripts:$PATH"' >> ~/.bashrc

More Precompiled Options

For ARM64, PPC64LE, and other architectures, visit mmseqs.com/hhsuite.

Compile HH-suite from source for custom configurations or MPI support.

Requirements

C/C++ compiler (GCC ≥ 4.8 or Clang ≥ 3.6)
CMake ≥ 2.8.12
Git

Compilation Steps

Clone Repository

git clone https://github.com/soedinglab/hh-suite.git
cd hh-suite

Create Build Directory

mkdir -p build && cd build

Configure with CMake

cmake -DCMAKE_INSTALL_PREFIX=. ..

CMake Options

-DCMAKE_BUILD_TYPE=Release - Build optimized binaries (default)
-DHAVE_MPI=1 - Enable MPI support for parallel processing
-DHAVE_SSE2=1 - Enable SSE2 optimizations
-DHAVE_AVX2=1 - Enable AVX2 optimizations (faster)

Compile and Install

make -j 4 && make install

Replace 4 with the number of CPU cores you want to use.

Update PATH

export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

macOS Compilation

The default macOS clang compiler doesn’t support OpenMP. Install GCC from Homebrew for multithreading support.

# Install GCC via Homebrew
brew install gcc

# Clone and build
git clone https://github.com/soedinglab/hh-suite.git
mkdir -p hh-suite/build && cd hh-suite/build

# Use GCC instead of clang
CC="$(brew --prefix)/bin/gcc-10" CXX="$(brew --prefix)/bin/g++-10" \
  cmake -DCMAKE_INSTALL_PREFIX=. ..

make -j 4 && make install
export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"

MPI Support

Only source-compiled versions support MPI, as MPI configuration is environment-specific.

To enable MPI for large-scale parallel searches:

cmake -DCMAKE_INSTALL_PREFIX=. -DHAVE_MPI=1 ..
make -j 4 && make install

Verify Installation

Confirm HH-suite is installed correctly:

hhblits -version

You should see version 3.3.0 and the help message.

Database Setup

HH-suite requires sequence or profile databases to search against. See the Databases section for:

Downloading prebuilt databases (Uniclust30, BFD, PDB70, Pfam)
Building custom databases
Database formats and requirements

Download Databases

Learn how to download and set up databases for HH-suite

Troubleshooting

Command not found after installation

Make sure the HH-suite binaries are in your PATH:

export PATH="/path/to/hhsuite/bin:/path/to/hhsuite/scripts:$PATH"

Add this to your ~/.bashrc or ~/.zshrc for persistence.

Illegal instruction error

You may be using an AVX2 build on a CPU that doesn’t support AVX2. Download the SSE2 build instead:

wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-SSE2-Linux.tar.gz

Slow performance on macOS

If you compiled with the default clang compiler, recompile using GCC from Homebrew to enable OpenMP multithreading support.

Permission denied when running Docker

Run Docker commands with sudo or add your user to the docker group:

sudo usermod -aG docker $USER

Then log out and log back in.

Next Steps

Quick Start

Run your first protein search

Download Databases

Set up sequence and profile databases

Getting Started

Core Tools

Utility Tools

Guides

Advanced

Prerequisites

Installation Methods

Verify Installation

Using Mamba (Faster)

Run HHblits with Docker

Interactive Docker Session

SSE2 Build (Compatible with older CPUs)

AVX2 Build (Recommended for modern CPUs)

More Precompiled Options

Requirements

Compilation Steps

macOS Compilation

MPI Support

Verify Installation

Database Setup

Download Databases

Troubleshooting

Next Steps

Quick Start

Download Databases

Build docs developers (and LLMs) love

Getting Started

Core Tools

Utility Tools

Guides

Advanced

​Prerequisites

​Installation Methods

​Verify Installation

​Using Mamba (Faster)

​Run HHblits with Docker

​Interactive Docker Session

​SSE2 Build (Compatible with older CPUs)

​AVX2 Build (Recommended for modern CPUs)

​More Precompiled Options

​Requirements

​Compilation Steps

​macOS Compilation

​MPI Support

​Verify Installation

​Database Setup

Download Databases

​Troubleshooting

​Next Steps

Quick Start

Download Databases

Build docs developers (and LLMs) love

Prerequisites

Installation Methods

Verify Installation

Using Mamba (Faster)

Run HHblits with Docker

Interactive Docker Session

SSE2 Build (Compatible with older CPUs)

AVX2 Build (Recommended for modern CPUs)

More Precompiled Options

Requirements

Compilation Steps

macOS Compilation

MPI Support

Verify Installation

Database Setup

Troubleshooting

Next Steps