Phylogenetic Network - serratus-bio/open-virome GitHub Wiki

A viral Phylogenetic Network or pnet is a graph representation made up of nodes of viruses, and edges of the pairwise evolutionary relationship between them.

Pnet Icon

The pnet graph

A pnet is represented as a weighted undirected, monopartite graph where:

  • Virus Node (hexagon): an abstract unit of virus, defined here as species-like Operational Taxonomic Units (sOTU) of RNA viruse (See: palmDB)
  • Edge (solid line): the alignment between two virus nodes. Global amino acid identity (aa %) generated by UCLUST all vs. all in range [0.3 - 0.9]
  • Edge (weight): line thickness is scaled by the inverse of alignment identity (distance)

Eimeria Virome Pnet

  • Example Eimeria pnet *

Summary stats

Total number of sOTU nodes: 513,176

Total number of Palmprint nodes: 562,283

Total number of sOTU SEQUENCE_SIMILARITY relationships: 26,341,751

Total number of SRA HAS_SOTU relationships: 8,687,315