SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses

(2015) Marie Lisandra Zepeda Mendoza et al.   BRIEFINGS IN BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

(2014) Genivaldo Gueiros Z. Silva et al.   PeerJ

Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals

(2013) Gizele D. Garcia et al.   MICROBIAL ECOLOGY

Polyketide Synthase Gene Diversity within the Microbiome of the Sponge Arenosclera brasiliensis, Endemic to the Southern Atlantic Ocean

(2012) Amaro E. Trindade-Silva et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Real Time Metagenomics: Using k-mers to annotate metagenomes

(2012) Robert A. Edwards et al.   BIOINFORMATICS

Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome

(2012) Louisi de Oliveira et al.   BMC GENOMICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN 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

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

(2012) Amaro E. Trindade-Silva et al.   PLoS One

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

(2012) Ramy K. Aziz et al.   PLoS One

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

(2011) Y. Zhao et al.   BIOINFORMATICS

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

(2010) Terry Disz et al.   BMC BIOINFORMATICS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

(2008) Elizabeth A. Dinsdale et al.   PLoS One