PHASTER: a better, faster version of the PHAST phage search tool

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

(2013) Janine Kamke et al.   ISME Journal

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Limin Fu et al.   BIOINFORMATICS

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Y. Zhao et al.   BIOINFORMATICS

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Prophinder: a computational tool for prophage prediction in prokaryotic genomes

(2008) Gipsi Lima-Mendez et al.   BIOINFORMATICS