PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Fast and flexible bacterial genomic epidemiology with PopPUNK

(2019) John A. Lees et al.   GENOME RESEARCH

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

(2019) Sion C Bayliss et al.   GigaScience

Population genomics of bacterial host adaptation

(2018) Samuel K. Sheppard et al.   NATURE REVIEWS GENETICS

Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

(2018) Harry A Thorpe et al.   GigaScience

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

(2014) Guillaume Méric et al.   PLoS One

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

(2014) Jason W. Sahl et al.   PeerJ

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter

(2012) Samuel K. Sheppard et al.   Genes

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS