pATLAS uses MASH to estimate the distances between all plasmids available in NCBI refseq database. However, only plasmid sequences that show a mash distance inferior to 0.1 (highly correlated with Average nucleotide identity (ANI) greater than 0.9) and are significantly associated (mash p-value<0.05) are linked in the plasmid network. All other plasmids are represented as an isolated node (singleton).
Each node in pATLAS represents a plasmid and its size relates to the number of base pairs of each plasmid in logarithmic scale . The links connect plasmids with approximately 90% average nucleotide identity.