Swarm: robust and fast clustering method for amplicon-based studies

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

(2013) Alexander F. Koeppel et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Limin Fu et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

(2012) Lucie Bittner et al.   MOLECULAR ECOLOGY

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

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

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

(2010) Markus Nebel et al.   Environmental Microbiology Reports

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY