A plugin for converting a cogent3 tree to ete3 tree object
Developed an app that takes a cogent3 PhyloNode then returns an ete3 PhyloTree, plus an app for edge colouring.
cogent3 to ete3 tree
from cogent3 import load_tree, get_app
from cogent3_ete3.style import show_legend
tree = load_tree("data/tree_large_scale.newick")
conv = get_app("cogent3_to_ete3")
t = conv(tree)
t is an ete3 PhyloTree.
colour edges by a mapping
The ete3_colour_edge app allows you to colour information on selected edges. The app applies a colour to named edges. This means for colouring internal edges the node must have names.
edge_to_cat = {"Vombatidae_Vombatus_ursinus": "A",
"Dasyuridae_Sarcophilus_harrisii": "B",
"Peramelidae_Echymipera_kalubu" : "C",
"Pseudochiridae_Pseudochirulus_forbesi": "D"}
cat_to_colour={"A":"blue",
"B":"blue",
"C":"red",
"D":"orange"}
cl = get_app("ete3_colour_edge", edge_to_cat=edge_to_cat, cat_to_colour=cat_to_colour)
t = cl(t)
You can use the convenient function to show a legend.
show_legend(t, cat_to_colour, legend_title="Your Category")
In the pop-up window, you can explore further and render the tree in a file as you progress:
1 maintainer
Metadata
1 maintainer
Release files for cogent3-ete3 2025.7.3
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| cogent3_ete3-2025.7.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 10.2 kB
Release files / cogent3_ete3-2025.7.3.tar.gz
| Download URL | cogent3_ete3-2025.7.3.tar.gz |
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| Tags | Python 3 |
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