This page will host selected and curated interactive network visualisations generated as part of the BAPS project. Each link opens a standalone PhageClouds HTML file.
Each PhageCloud is an interactive network representation of related phage genomes.
Nodes
Node information
Hovering over a genome displays its accession, name, number of genes, genome size, and a direct link to the relevant NCBI entry.
Phages used in Phage Therapy cases have a magenta border
Edges
Genomes are connected based on pairwise Mash distances. Thicker edges indicate higher sequence similarity.
Interaction
A PhageCloud is an interactive network view of related phage genomes. Nodes represent genomes and edges represent sequence similarity based on Mash distances.
Circles are complete phage genomes from NCBI. Squares are BAPS derived phages identified within bacterial genome assemblies.
Node size is proportional to genome length.
Colours indicate the annotated host associated with each genome.
Edges connect genomes based on pairwise Mash distances. Thicker edges indicate higher sequence similarity, while thinner edges indicate more distant relationships.
For the Phage Therapy PhageClouds, a mash distance threshold of ≤ 0.1 was applied. For all other PhageClouds, a threshold of ≤ 0.2 was used.
BAPS identifies complete lytic phage genomes that occur within bacterial genome assemblies at NCBI. The host is known because it is the organism used for the assembly.
Large-scale analysis of bacterial genomes reveals thousands of lytic phages.
Perfilyev A, Gæde A, Hooton S, Zahran SA, Kalatzis PG, Winther-Have CS,
Ibarra Chavez R, Wilkinson RC, Thanki AM, Liu Z, Zhang Q, Lv Q, Liu Y,
Gigante AM, Atterbury RJ, Petersen B, Millard AD, Clokie MRJ,
Sicheritz-Pontén T.
Nature Microbiology. 2026 Jan;11(1):42–52.
From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage
Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.
Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A,
Petersen B, Clokie MRJ, Sicheritz-Pontén T.
Phage (New Rochelle). 2021 Dec;2(4):194–203.
This usually occurs because the underlying bacterial genome assembly is fragmented. In such cases, the phage genome may be split across several contigs within the same assembly, resulting in multiple smaller representations that together correspond to the full expected genome size.
When hovering over a node, each phage genome and BAPS has a direct link to NCBI.
Large clouds can be heavy in a browser. Try reloading the page, closing other tabs, or using a desktop browser. You can also zoom out and drag clusters rather than individual nodes.
Hover to view details and links. Drag nodes to rearrange the layout. Zoom using the trackpad two finger gesture or mouse wheel.