trees.md

Phylogenetic Trees

Phylogenetic tree visualization functions including basic tree plots, circular layouts, unrooted trees, tree comparisons, and tree annotations.

Functions

plot_phylo_tree(tree, *, ax=None)

Plot a Biopython Phylo tree to matplotlib Axes.

Example:

from pathlib import Path
from metainformant.dna import sequences, phylogeny
from metainformant.visualization import plot_phylo_tree

seqs = sequences.read_fasta(str(Path("tests/data/dna/toy.fasta")))
tree = phylogeny.neighbor_joining_tree(seqs)
ax = plot_phylo_tree(tree)

circular_tree_plot(tree, *, ax=None)

Plot a phylogenetic tree in circular layout.

unrooted_tree_plot(tree, *, ax=None)

Plot an unrooted phylogenetic tree.

tree_comparison_plot(trees, labels=None, *, ncols=2, figsize=None)

Plot multiple trees side by side for comparison.

tree_annotation_plot(tree, annotations=None, *, ax=None, **kwargs)

Plot a phylogenetic tree with annotations.

Cross-links

• Build trees in DNA: Phylogeny and render here.