AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks

The Two Lives of Bacillus thuringiensis: Response to Ruan et al. and Loguercio and Argôlo-Filho

(2016) Niels Bohse Hendriksen   TRENDS IN MICROBIOLOGY

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

(2012) Joakim Ågren et al.   PLoS One

Defining Pathogenic Bacterial Species in the Genomic Era

(2011) Kalliopi Georgiades et al.   Frontiers in Microbiology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS