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.

Sign up for GitHub

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

Jump to bottom

Indices - add length to most recent common ancestor #763

Closed
shawnlaffan opened this issue Jun 17, 2020 · 2 comments
Closed

Indices - add length to most recent common ancestor #763

shawnlaffan opened this issue Jun 17, 2020 · 2 comments
Assignees
@shawnlaffan
Labels
enhancement indices
Milestone
Release_4.0

Comments

@shawnlaffan
Copy link
Owner

This index would give the length from the terminals and/or the root of the tree.

As a bonus its calculation would give the proportional positions relative to the total length of the tree and/or to the terminal branch in the set of labels that is furthest from the root.
@shawnlaffan shawnlaffan self-assigned this Jun 17, 2020
@shawnlaffan shawnlaffan added this to the Release_4.0 milestone Jun 17, 2020
shawnlaffan added a commit that referenced this issue Jun 18, 2020
@shawnlaffan
Indices: add local PD calculation
22656aa 
Includes tests.

Updates #762

Also includes sub to get the last shared ancestor
from a subtree, which is the initial work for #763
shawnlaffan added a commit that referenced this issue Jun 19, 2020
@shawnlaffan
Indices: add calc_last_shared_ancestor
f2fe550 
This provides information about the last (youngest)
shared ancestor for an assemblage.

Updates #763
@shawnlaffan
Copy link
Owner Author

Mark as complete.

shawnlaffan added a commit that referenced this issue Jun 25, 2020
@shawnlaffan
local PD: handle single terminals better
0cd0fe2 
Dist to tips should be zero, whereas we
were getting negatives in some cases.

Updates #763
shawnlaffan added a commit that referenced this issue Jun 25, 2020
@shawnlaffan
local PD: add test for single lineage samples
4cde400 
Updates #763
@shawnlaffan
Copy link
Owner Author

Now it should be complete.

@shawnlaffan shawnlaffan mentioned this issue Jun 27, 2020
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@shawnlaffan shawnlaffan

Labels
enhancement indices
Projects
None yet
Milestone
Release_4.0
Development

No branches or pull requests
1 participant
@shawnlaffan