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Explore use of IQ-TREE's constraint tree option #79
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This is how it's used right now in the SC2 reference tree workflow: Simply add constraint tree file path after 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:
Both 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:
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