SARS-CoV-2 Genome Tree

How SARS-CoV-2 trees are constructed in Pathogenwatch.


Pathogenwatch will automatically generate a tree of SARS-CoV-2 genomes when a collection is created from the Genome Browser. When each genome is uploaded to Pathogenwatch an alignment against the Wuhan Hu 1 reference genome is stored. The selected genomes are aligned into a multiple sequence alignment and a dendrogram produced using FastTree. This tree is then displayed in the interactive collection viewer.



Tree Building

  • The FASTA files are concatenated into a multiple sequence alignment along with the wuhan-hu-1 reference.

  • Run FastTree with the options -gtr -nosupport -nt.

  • Root the resulting tree to the reference.

  • Remove the reference from the tree.


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