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Table of Contents Foldseek User Guide

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• Summary
• System requirements
• Installation
• Getting started
  • Easy workflows
  • Downloading databases
  • Searching
• Optimizing sensitivity and consumption of resources
• Frequently Asked Questions

Summary

System requirements

Foldseek runs on modern UNIX operating systems and is tested on Linux and macOS. Additionally, we are providing a preview version for Windows.

Foldseek takes advantage of multi-core systems through OpenMP and uses the SIMD capabilities of the system. Optimal performance requires a system supporting the AVX2 instruction set, however SSE4.1 and very old systems with SSE2 are also supported. It also supports the PPC64LE and ARM64 processor architectures, these require support for the AltiVec or NEON SIMD instruction sets, respectively.

To check if Foldseek supports your system execute the following commands, depending on your operating system:

Check system requirements under Linux

[ $(uname -m) = "x86_64" ] && echo "64bit: Yes" || echo "64bit: No"
grep -q avx2 /proc/cpuinfo && echo "AVX2: Yes" || echo "AVX2: No"
grep -q sse4_1 /proc/cpuinfo && echo "SSE4.1: Yes" || echo "SSE4.1: No"
# for very old systems which support neither SSE4.1 or AVX2
grep -q sse2 /proc/cpuinfo && echo "SSE2: Yes" || echo "SSE2: No"

Check system requirements under macOS

[ $(uname -m) = "x86_64" ] && echo "64bit: Yes" || echo "64bit: No"
sysctl machdep.cpu.leaf7_features | grep -q AVX2 && echo "AVX2: Yes" || echo "AVX2: No"
sysctl machdep.cpu.features | grep -q SSE4.1 && echo "SSE4.1: Yes" || echo "SSE4.1: No"

Installation

Foldseek can be installed for Linux or macOS

(1) downloading a statically compiled version For Linux computer with supports AVX2 use:

wget https://mmseqs.com/foldseek/foldseek-linux-avx2.tar.gz
tar xvzf foldseek-linux-avx2.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH

Linux with SSE4.1

wget https://mmseqs.com/foldseek/foldseek-linux-sse41.tar.gz
tar xvzf foldseek-linux-sse41.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH

macOS build (universal binary with SSE4.1/AVX2/M1 NEON)

wget https://mmseqs.com/foldseek/foldseek-osx-universal.tar.gz
tar xvzf foldseek-osx-universal.tar.gz
export PATH=$(pwd)/foldseek/bin/:$PATH

(2) using bioconda

conda install -c conda-forge -c bioconda foldseek

(3) compiling the from source (see below),

Compile from source under Linux

Compiling Foldseek from source has the advantage that it will be optimized to the specific system, which should improve its performance. To compile Foldseek git, g++ (4.9 or higher) and cmake (2.8.12 or higher) are needed. Afterwards, the foldseek binary will be located in build/bin/.

git clone https://github.com/steineggerlab/foldseek.git
cd foldseek
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make
make install 
export PATH=$(pwd)/bin/:$PATH

See the Customizing compilation through CMake section if you compile Foldseek on a different system than the one where it will eventually reun.

Compile from source under macOS

Compiling under Clang

To compile Foldseek with (Apple-)Clang you need to install either XCode or the Command Line Tools. You also need libomp. We recommend installing it using Homebrew:

brew install cmake libomp zlib bzip2

CMake currently does not correctly identify paths to libomp. Use the script in util/build_osx.sh to compile Foldseek. The resulting binary will be placed in OUTPUT_DIR/mmseqs.

./util/build_osx.sh PATH_TO_FOLDSEEK_REPO OUTPUT_DIR

Compiling using GCC

Please install the following packages with Homebrew:

brew install cmake gcc@10 zlib bzip2

Use the following cmake call:

CC="gcc-10" CXX="g++-10" cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..