Links

Core Genome Tree

About

For a curated set of species Pathogenwatch provides the ability to construct a tree based on a core genome distance, along with assignment to a closest reference genome in a taxonomically representative set. The core genome and parameters are tested for each in species in turn, using a combination of manual validation against published datasets and automated validation against "gold standard" trees.

Methods

The approach can be split into four separate stages, described in their own sections:
  1. 1.
    ​Core Assignment ​
  2. 2.
  3. 3.
    ​Filtering​
  4. 4.
    ​Tree Construction​