-
The conda method for installation doesn't seem to work and I ran into the same error messages as a previous issue post, but the pip install method worked fine. However, I am unable to run python testd…
-
Hi,
I tried to load a newick tree with internal node names with `ete3 mod`, but when I add `--src_tree_format=1` , it is totally ignored.
The newick file is the following:
```
(
Cavia_porc…
-
Advanced Newick formats support punctuation in _quoted_ labels;
> Unquoted labels may not contain blanks, parentheses, square brackets, single_quotes, colons, semicolons, or commas.
— http://ev…
-
Is there a way to speed up this conversion, specifically with `ToNewick`?
```
library(ape)
data(bird.families)
system.time(bf
-
I am trying to export my tree in newick format for subsequent analysis in TreeTimer. I choose "Save as currently displayed" as I would like to save the tree after rerooting it in FigTree. Howeve…
-
Hi
A minor issue; in the Newick parser read_newick function (parsers/newick.py, line 220) called when reading newick files, as described here:
http://etetoolkit.org/docs/latest/tutorial/tutorial_t…
-
see https://github.com/dib-lab/charcoal/commit/4838253a5677e3c64e50cd621308772116bbea81 for example code
-
I wrote a script to convert a multisearch output CSV to a Newick file. It performs hierarchical clustering using the `ward` linkage method.
```python
import csv
import networkx as nx
import nu…
-
Hi, I am using Biopython 1.79.
Sorry, I admit this is a detail, but I reference it in case comment parsing is updated in the future. I could participate in that.
### Expected behaviour
Commen…
-
How it might work:
1. Get taxonomic information from the database in a kingdom/phylum/class/order/family/genus table format. This could be done via templating (slow) or ajax (more complicated?).
2. Tu…