Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add get_node_time function #34

Closed

Conversation

Billyzhang1229
Copy link
Contributor

This PR will fix to_newick() function when there is no time array.

@coveralls
Copy link

Pull Request Test Coverage Report for Build 2819084879

  • 24 of 24 (100.0%) changed or added relevant lines in 3 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.3%) to 97.826%

Totals Coverage Status
Change from base Build 2816757015: 0.3%
Covered Lines: 495
Relevant Lines: 506

💛 - Coveralls

@jeromekelleher
Copy link
Owner

This is assuming that all leaves are at time 0, though, which isn't always the case. This is quite tricky because there are many cases where we don't actually know the node times, and it's just the branch lengths that are estimated. This is when then root isn't necessarily known either (and the rooting is abitrary). We want to support these types of tree in phylokit, which is why the node_time array isn't mandatory (and why it's not computed by default for the newick output).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants