Comments (1)
corneliusroemer
commented on July 19, 2024
This is how it's used right now in the SC2 reference tree workflow:
Simply add constraint tree file path after -g to tree builder args:
https://github.com/neherlab/nextclade_data_workflows/blob/09be86c1718ffab2deed7060c3f7a70c135c530d/sars-cov-2/defaults/parameters.yaml#L22
And that's the hand coded tree: https://github.com/neherlab/nextclade_data_workflows/blob/feat/gisaid-v2/sars-cov-2/defaults/constraint.nwk
In the flu case, there are two options:
- Either you get (synthetic) prototypical sequences for each clade with constant names, like
2A,2A.1etc. (similar to the SC2 workflow) and hand code a short Newick tree with the right topology - Or you generate a constraint tree using actual sequence names based on the topology as revealed through clade-hierarchies or handcoded in a newick tree that's read in by Biopython.Phylo
Both approaches should work.
from seasonal-flu.
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from seasonal-flu.