feat: re-add 'unrooted' argument to cophenetic distances#98
Merged
Neclow merged 1 commit intosbhattlab:mainfrom Aug 7, 2025
Merged
feat: re-add 'unrooted' argument to cophenetic distances#98Neclow merged 1 commit intosbhattlab:mainfrom
Neclow merged 1 commit intosbhattlab:mainfrom
Conversation
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Reinstate the "unrooted" option for cophenetic distances to match ete3. This might be useful for BME applications.
Note: comparing the "unrooted" option for phylo2vec with branch lengths requires a special kind of unrooting. ete3 simply deletes the first children that is not a leaf, while we remove the node with the largest label (which has to be a non-leaf for n_leaves > 2).
Supersedes #97