This interface allows the user to define a set of genomes and displays a tree showing the genomic similarity.

The genomic similarity is estimated using Mash, a software that computes a distance between two genomes. This distance is correlated to the ANI like: D ≈ 1-ANI

From all the pairwise distances of the genomes set, a tree is construct dynamically using the neighbor-joining javascript package.

The tree displays clustering annotations. This clustering has been computed from all-pairs distances ≤ 0.06 (≈94% ANI) that correspond to the ANI standard to define a species group.

The clustering has been computed using the Louvain Community Detection.

This interface allows the user to search for common OR specific genes/regions between a query genome/replicon and other genomes/replicons chosen from the ones available in our PkGDB database (i.e, (re)annotation of bacterial genomes or complete proteome downloaded from the RefSeq/WGS sections).

This interface allows the user to search for potentially horizontally transferred genes (HGT) which are gathered in genomic regions (Region of Genomic Plasticity). The RGP_Finder method first starts with the identification of synteny breaks between a query genome and other close genomes chosen from the ones available in our PkGDB database. Then it searches for HGT features (tRNA hotspot, mobility genes), and for compositional bias (AlienHunter (Vernikos and Parkhill, 2006), SIGI-HMM (Waack et al., 2006), and GC deviation computation) in the query genome. RGP_Finder is able to characterize genomic regions presenting both to a synteny break and several features specific to Genomic Islands, regions with HGT features only, and regions associated with synteny break only. The graphical interfaces associated to this tool are useful to explore in detail the predicted regions, using also the comparative genomic context available in MaGe.