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Nature Communications|July 1, 2018
Clustering huge protein sequence sets in linear timeMartin Steinegger, Johannes SödingBioinformatics (Oxford, England)|January 9, 2016
MMseqs software suite for fast and deep clustering and searching of large protein sequence setsMaria Hauser, Martin Steinegger, Johannes SödingNature Methods|June 26, 2019
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfoldMartin Steinegger, Milot Mirdita, Johannes SödingBioinformatics (Oxford, England)|January 8, 2019
MMseqs2 desktop and local web server app for fast, interactive sequence searchesMilot Mirdita, Martin Steinegger, Johannes SödingBMC Bioinformatics|September 16, 2019
HH-suite3 for fast remote homology detection and deep protein annotationMartin Steinegger, Markus Meier, Milot Mirdita, et al.Microbiome|October 1, 2024
Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAsAnnika Jochheim, Florian A Jochheim, Alexandra Kolodyazhnaya, et al.Nucleic Acids Research|December 1, 2016
Uniclust databases of clustered and deeply annotated protein sequences and alignmentsMilot Mirdita, Lars von den Driesch, Clovis Galiez, et al.Genome Biology|October 28, 2025
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasetsLouis Kraft, Johannes Söding, Martin Steinegger, et al.Current Protocols in Bioinformatics|December 14, 2020
Protein Sequence Analysis Using the MPI Bioinformatics ToolkitFelix Gabler, Seung-Zin Nam, Sebastian Till, et al.Bioinformatics (Oxford, England)|November 9, 2004
Protein homology detection by HMM-HMM comparisonJohannes SödingPageof 16