MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
The MMseqs2 user guide is available in our GitHub Wiki or as a PDF file (Thanks to pandoc!). The wiki also contains tutorials to learn how to use MMseqs2 with real data. For questions please open an issue on GitHub or ask in our chat. Keep posted about MMseqs2/Linclust updates by following Martin on Twitter.
MMseqs2 can be used by compiling from source, downloading a statically compiled version, using Homebrew, conda or Docker. MMseqs2 requires a 64-bit system (check with uname -a | grep x86_64
) with at least the SSE4.1 instruction set (check by executing cat /proc/cpuinfo | grep sse4_1
on Linux or sysctl -a | grep machdep.cpu.features | grep SSE4.1
on MacOS).
# install by brew
brew install mmseqs2
# install via conda
conda install -c conda-forge -c bioconda mmseqs2
# install docker
docker pull soedinglab/mmseqs2
# static build with SSE4.1
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz; tar xvfz mmseqs-linux-sse41.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH
# static build with AVX2
wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz; tar xvfz mmseqs-linux-avx2.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH
The AVX2 version is faster than SSE4.1, check if AVX2 is supported by executing cat /proc/cpuinfo | grep avx2
on Linux and sysctl -a | grep machdep.cpu.leaf7_features | grep AVX2
on MacOS).
We also provide static binaries for all supported platforms at mmseqs.com/latest.
MMseqs2 comes with a bash command and parameter auto completion, which can be activated by adding the following lines to your $HOME/.bash_profile:
if [ -f /Path to MMseqs2/util/bash-completion.sh ]; then source /Path to MMseqs2/util/bash-completion.sh fi
Compiling MMseqs2 from source has the advantage that it will be optimized to the specific system, which should improve its performance. To compile MMseqs2 git
, g++
(4.8 or later) and cmake
(2.8.12 or later) are needed. Afterwards, the MMseqs2 binary will be located in the build/bin/
directory.
git clone https://github.com/soedinglab/MMseqs2.git
cd MMseqs2
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make -j 4
make install
export PATH=$(pwd)/bin/:$PATH
❗ Compiling MMseqs2 correctly on macOS requires more effort.
We provide easy
workflows to cluster, search and assign taxonomy. These easy
workflows are a shorthand to deal directly with FASTA/FASTQ files as input and output. MMseqs2 provides many modules to transform, filter, execute external programs and search. However, these modules use the MMseqs2 database formats, instead of the FASTA/FASTQ format. For maximum flexibility, we recommend using MMseqs2 workflows and modules directly. Please read more about this in the documentation.
For clustering, MMseqs2 easy-cluster
and easy-linclust
are available.
easy-cluster
by default clusters the entries of a FASTA/FASTQ file using a cascaded clustering algorithm.
mmseqs easy-cluster examples/DB.fasta clusterRes tmp --min-seq-id 0.5 -c 0.8 --cov-mode 1
easy-linclust
clusters the entries of a FASTA/FASTQ file. The runtime scales linearly with input size. This mode is recommended for huge datasets.
mmseqs easy-linclust examples/DB.fasta clusterRes tmp
Sequence identity is by default estimated to output real sequence identity use --alignment-mode 3
.
Read more about the clustering format in our user guide.
Please adjust the clustering criteria and check if temporary directory provides enough free space. For disk space requirements, see the user guide.
The easy-search
workflow searches directly with a FASTA/FASTQ files against either another FASTA/FASTQ file or an already existing MMseqs2 database.
mmseqs easy-search examples/QUERY.fasta examples/DB.fasta alnRes.m8 tmp
It is also possible to pre-compute the index for the target database. This reduces overhead when searching repeatedly against the same database.
mmseqs createdb examples/DB.fasta targetDB
mmseqs createindex targetDB tmp
mmseqs easy-search examples/QUERY.fasta targetDB alnRes.m8 tmp
The databases
workflow provides download and setup procedures for many public reference databases, such as the Uniref, NR, NT, PFAM and many more (see Downloading databases). For example, to download and search against a database containing the Swiss-Prot reference proteins run:
mmseqs databases UniProtKB/Swiss-Prot swissprot tmp
mmseqs easy-search examples/QUERY.fasta swissprot alnRes.m8 tmp
The speed and sensitivity of the search
can be adjusted with -s
parameter and should be adapted based on your use case (see setting sensitivity -s parameter). A very fast search would use a sensitivity of -s 1.0
, while a very sensitive search would use a sensitivity of up to -s 7.0
. A detailed guide how to speed up searches is here.
The output can be customized with the --format-output
option e.g. --format-output "query,target,qaln,taln"
returns the query and target accession and the pairwise alignments in tab separated format. You can choose many different output columns.
The easy-taxonomy
workflow can be used to assign sequences taxonomical labels. It performs a search against a sequence database with taxonomy information (seqTaxDb), chooses the most representative sets of aligned target sequences according to different strategies (according to --lca-mode
) and computes the lowest common ancestor among those.
mmseqs createdb examples/DB.fasta targetDB
mmseqs createtaxdb targetDB tmp
mmseqs createindex targetDB tmp
mmseqs easy-taxonomy examples/QUERY.fasta targetDB alnRes tmp
By default, createtaxdb
assigns a Uniprot accession to a taxonomical identifier to every sequence and downloads the NCBI taxonomy. We also support BLAST, SILVA or custom taxonomical databases. Many common taxonomic reference databases can be easily downloaded and set up by the databases
workflow.
Read more about the taxonomy format and the classification in our user guide.
MMseqs2 provides many additional search modes:
- Iterative sequences-profile searches (like PSI-BLAST) with the
--num-iterations
parameter - Translated searches of nucleotides against proteins (blastx), proteins against nucleotides (tblastn) or nucleotide against nucleotide (tblastx)
- Iterative increasing sensitivity searches to find only the best hits faster
- Taxonomic assignment using 2bLCA or LCA
- Fast ungapped alignment searches to find very similar sequence matches
- Very fast and sensitive searches against profile databases such as the PFAM
- Reciprocal best hits search
- Web search API and user interface
Many modes can also be combined. You can, for example, do a translated nucleotide against protein profile search.
MMseqs2 minimum memory requirements for cluster
or linclust
is 1 byte per sequence residue, search
needs 1 byte per target residue. Sequence databases can be compressed using the --compress
flag, DNA sequences can be reduced by a factor of ~3.5
and proteins by ~1.7
.
MMseqs2 checks the available system memory and automatically divides the target database in parts that fit into memory. Splitting the database will increase the runtime slightly. It is possible to control the memory usage using --split-memory-limit
.
MMseqs2 can run on multiple cores and servers using OpenMP and Message Passing Interface (MPI). MPI assigns database splits to each compute node, which are then computed with multiple cores (OpenMP).
Make sure that MMseqs2 was compiled with MPI by using the -DHAVE_MPI=1
flag (cmake -DHAVE_MPI=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
). Our precompiled static version of MMseqs2 cannot use MPI. The version string of MMseqs2 will have a -MPI
suffix, if it was built successfully with MPI support.
To search with multiple servers, call the search
or cluster
workflow with the MPI command exported in the RUNNER environment variable. The databases and temporary folder have to be shared between all nodes (e.g. through NFS):
RUNNER="mpirun -pernode -np 42" mmseqs search queryDB targetDB resultDB tmp