cogent3-ete3 2025.6.27

cogent3 plugin for ete3

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: