MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Lambda: the local aligner for massive biological data

(2014) Hannes Hauswedell et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA

(2013) D. H. Huson et al.   BIOINFORMATICS

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

PSimScan: Algorithm and Utility for Fast Protein Similarity Search

(2013) Anna Kaznadzey et al.   PLoS One

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude

(2012) Joshua Tan et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

(2010) Daniel Chubb et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS