Open joverlee521 opened 2 years ago
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:
2A
, 2A.1
etc. (similar to the SC2 workflow) and hand code a short Newick tree with the right topologyBoth approaches should work.
@corneliusroemer experimented with IQ-TREE's constraint tree option to prevent IQ-TREE from putting clades in the wrong place for NextClade reference trees. This seems like a good way to ensure correct trees especially in 6m builds that may be lacking context sequences.
One issue brought up in initial Slack thread: