Changing default reference


Is it possible to change the root of the tree (the reference sequence) without having to change other default settings as much as possible? I tried assigning the “reference” manually, but it appears that the default ref is used in more than one place and the code doesn’t work properly by changing just that.


Hi @Sanna - you are correct that various references are used in different places, but the sequence used to root the tree should be easy to change. This may be specified in your builds.yaml via:

  root: "Wuhan/Hu-1/2019"

(“Wuhan/Hu-1/2019” is the default root.)