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

QRTD Quartet Distance #46

Open
weka511 opened this issue Nov 11, 2020 · 1 comment
Open

QRTD Quartet Distance #46

weka511 opened this issue Nov 11, 2020 · 1 comment
Assignees
@weka511
Labels
New Feature

Comments

@weka511
Copy link
Owner

weka511 commented Nov 11, 2020

No description provided.

@weka511 weka511 self-assigned this Nov 11, 2020
weka511 added a commit that referenced this issue Nov 11, 2020
@weka511
#46 Started work on qrtd
4ad6429
@weka511 weka511 mentioned this issue Nov 16, 2020
Closed
weka511 added a commit that referenced this issue Nov 25, 2020
@weka511
#46: passes sample
f65a6c3
weka511 added a commit that referenced this issue Nov 25, 2020
@weka511
#46 tidied up. Times out on Rosalind data
5f55dfc
weka511 added a commit that referenced this issue Nov 26, 2020
@weka511
#46 Times out on Rosalind data
de90ead
weka511 added a commit that referenced this issue Dec 18, 2020
@weka511
Added issue numbers for WIP #45, #46, #48, #49
fc6ec0d
weka511 added a commit that referenced this issue Dec 22, 2020
@weka511
#46. Refactored. Still slow, and inaccurate for sample
68b2ea6
weka511 added a commit that referenced this issue Dec 22, 2020
@weka511
#46. Refactored. Still slow, and inaccurate for sample
4553817
@weka511 weka511 removed their assignment Jan 25, 2021
weka511 added a commit that referenced this issue Mar 20, 2023
@weka511
#46 Created unit test
122f2bc
@weka511 weka511 self-assigned this Mar 25, 2023
weka511 added a commit that referenced this issue Mar 25, 2023
@weka511
#46 Moved newick parser to newick.py
d86e6a2
weka511 added a commit that referenced this issue Mar 25, 2023
@weka511
#46 Print tree for debugging
2909a92
weka511 added a commit that referenced this issue Mar 29, 2023
@weka511
#46 started hierarchical decomposition
68be490
weka511 added a commit that referenced this issue Mar 29, 2023
@weka511
#46 hierarchical decomposition complete
e25746f
weka511 added a commit that referenced this issue Mar 29, 2023
@weka511
#46 Change root of T1 as described in Figure 9
d804b6a
weka511 added a commit that referenced this issue Apr 1, 2023
@weka511
#46 started decorating tree
60beedd
weka511 added a commit that referenced this issue Apr 2, 2023
@weka511
#46 Add colours to leaves
9e2562a
weka511 added a commit that referenced this issue Apr 3, 2023
@weka511
#46 compute F3
a3ed8f3
weka511 added a commit that referenced this issue Apr 5, 2023
@weka511
#46 Started to implement Bryant et al
4a5d903
weka511 added a commit that referenced this issue Apr 6, 2023
@weka511
#46 WIP
57cfd98
weka511 added a commit that referenced this issue Apr 7, 2023
@weka511
#46 Use Bryant el at for sample test
51597f4
weka511 added a commit that referenced this issue Apr 8, 2023
@weka511
#46 Moved qrtd(...) to phylogeny.py
29c1986
weka511 added a commit that referenced this issue Apr 8, 2023
@weka511
#46 Refactored to reduce memory usage
d916ec3
weka511 added a commit that referenced this issue Apr 10, 2023
@weka511
#46 Converted to use numpy; still way too slow on --rosalind
50ca4b5
weka511 added a commit that referenced this issue Apr 10, 2023
@weka511
#46 Removed a bunch of dead code
3dd5d91
weka511 added a commit that referenced this issue Apr 10, 2023
@weka511
#46 Tidied up and added some doco
3883b3d
@weka511 weka511 mentioned this issue Apr 19, 2023
Closed
@weka511
Copy link
Owner Author

weka511 commented Apr 21, 2023

Changed to Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees, Andreas Sand et al. Answer is not correct, but program is must faster (although not enough) Elapsed Time 5 m 10.27 s

weka511 added a commit that referenced this issue Apr 21, 2023
@weka511
#46 Use Sand et al for qrtd
b8a9104
weka511 added a commit that referenced this issue Apr 21, 2023
@weka511
#46 Cosmetic changes
9d1ca9c
weka511 added a commit that referenced this issue Apr 23, 2023
@weka511
#46 Sample test passes using Sand et al
3e17ea4
weka511 added a commit that referenced this issue Apr 26, 2023
@weka511
#46 test data (still failing)
c0e7efe
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@weka511 weka511

Labels
New Feature
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@weka511