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:
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