Phylen: automatic phylogenetic reconstruction using the EggNOG database

High-throughput sequencing is dramatically increasing the amount of genetic data available from all domains of life, but particularly from bacteria. The smaller size of bacterial genomes allows to sequence large collections of strains, mainly from species that deserve interest for their importance as human or farm animal pathogens. Phylogenetic analysis has become a standard tool to understand the evolutionary history, epidemiology and virulence of these bacteria, and the availability of genomic information has allowed to move from single-gene (e.g. using the 16S rRNA gene) to multilocus or core genome trees that bring us closer to a more reliable reconstruction of phylogenetic structure.