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It may be better to use a phyogenetic based distance software. Many exist including ape:
```bash
library(ape)
# Load your phylogenetic tree (Newick format or other)
tree
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Running the `plot_njt()` function on larger datasets can take upwards of 20 minutes or more specifically in the stage after the pairwise distances have been computed and during the construction of the…
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Create function that calculates RF distances between 2 phylogenetic trees.
You will need to read slides 55-58 and 60 from merged lectures posted by me on slack and details from https://rdrr.io/cran/a…
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There is an undirected connected tree with `n` nodes labeled from `0` to `n - 1` and `n - 1` edges.
You are given the integer `n` and the array `edges` where `edges[i] = [ai, bi]` indicates that th…
F4NT0 updated
5 months ago
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There's a possible issue with the current implementation of [`scale_by_optimistic_gradient`](https://optax.readthedocs.io/en/latest/api/transformations.html#optax.scale_by_optimistic_gradient). At the…
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### Question Validation
- [X] I have searched both the documentation and discord for an answer.
### Question
# The tree traversal retrieval method in RAPTOR differs from the approach outlined in th…
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Using the attached alignment and this code within a jupyter notebook
```python
from cogent3 import get_app, load_aligned_seqs
aln = load_aligned_seqs("ENSG00000000971.fa", moltype="dna")
phylo…
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### Bug summary
When packaging librosa 0.10.2.post1 (from tarball from GitHub) for openSUSE, the test suite fails in `test_beat` and `test_beat_units` tests:
```
[ 154s] [gw35] [ 98%] FAILED tes…
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First, thanks for this extremely useful package and detailed explanations on tree metrics and visualizations in treespace as well as assessments of those visualizations.
I have a question about the…
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Hi @DavisVaughan, thanks so much for your great tree-sitter work. For an upcoming project at rOpenSci, we aim to use tree-sitter s-expression output to quantify aspects of tree edit distances between …