Comparative Genomics Tools
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
The tree displays clustering annotations. This clustering has been computed from all-pairs distances ≤ 0.06 (≈94% ANI) that correspond to the ANI standart to define a species group.
The clustering has been computed using the Louvain Community Detection.
It allows the users to:
- Compute pan-genome and core-genome sizes and their evolutions for a genome set
- Determine the common and variable genome proportion for each genome
- Exclude the pan, core and variable-genome of another genome set to the analysis
- Extract core-genome, variable-genome and strain specific sequences and annotations.