Hotfix: Infer ancestral root in the phylogenetic workflow #61
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This commit reverts the change introduced in 9431655 which set the REFSEQ references as the roots in the auspice trees. Turns out this is not the desired behavior for the dengue phylogenetic trees. Instead, we want to use the sequences and metadata to infer the ancestral root of each tree. These inferred-ancestral roots will then be used in building the nextclade datasets as hard-coded reference and root of the scaffold trees.
genehack
approved these changes
Jun 4, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
This commit reverts the change introduced in 9431655 which set the REFSEQ references as the roots in the auspice trees. Turns out this is not the desired behavior for the dengue phylogenetic trees.
Instead, we want to use the sequences and metadata to infer the ancestral root of each tree. These inferred-ancestral roots can then be used in building the nextclade datasets as hard-coded reference and root of the scaffold trees.
Related issue(s)
Checklist