MMseqs specifications

Information


Unique identifier OMICS_11001
Name MMseqs
Alternative names Many-against-Many sequence searching, MMseqs2
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Johannes Soeding
  • person_outline Martin Steinegger

Additional information


A GUI version is available at https://github.com/soedinglab/MMseqs2-App https://github.com/soedinglab/MMseqs2/wiki

Information


Unique identifier OMICS_11001
Name MMseqs
Alternative names Many-against-Many sequence searching, MMseqs2
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Download


github.png

Documentation


Maintainers


  • person_outline Johannes Soeding
  • person_outline Martin Steinegger

Additional information


A GUI version is available at https://github.com/soedinglab/MMseqs2-App https://github.com/soedinglab/MMseqs2/wiki

Publications for Many-against-Many sequence searching

MMseqs citations

 (2)
library_books

HipMCL: a high performance parallel implementation of the Markov clustering algorithm for large scale networks

2018
Nucleic Acids Res
PMCID: 5888241
PMID: 29315405
DOI: 10.1093/nar/gkx1313

[…] nd at 70% length coverage bidirectionally for all the predicted proteins of the isolate genomes stored in IMG (Isolates 1, 2 and 3) and (ii) similarities of proteins in Metaclust50 (https://metaclust.mmseqs.com/) dataset which contains predicted genes from metagenomes and metatranscriptomes of assembled contigs from IMG/M and NCBI. For the three isolate datasets, we used different LAST parameters […]

library_books

Gearing up to handle the mosaic nature of life in the quest for orthologs

2017
Bioinformatics
PMCID: 5860199
PMID: 28968857
DOI: 10.1093/bioinformatics/btx542

[…] ph. Hieranoid () achieves linear scaling to the number of species by aggregating orthologs along a species guide tree. Another approach dealing with a similar problem was presented in the form of the MMseqs many-versus-many sequence comparison software (). Still other approaches were suggested, such as making use of the nested nature of taxonomy and the transitive property of homology for more rap […]

MMseqs institution(s)
Quantitative and Computational Biology group, Max-Planck Institute for Biophysical Chemistry, Gottingen, Germany; Department of Chemistry, Seoul National University, Seoul, Korea
MMseqs funding source(s)
Supported by the European Research Council in the framework of its Horizon 2020 Framework Programme for Research and Innovation (grant “VirusX”, project no. 685778).

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