Phylo Module

The phylo module provides functions for phylogenetic tree construction and analysis.

Core Functions

neighbor_joining(distance_matrix[, outgroup])

Construct phylogenetic tree using neighbor-joining algorithm.

Utility Functions

Function Details

Phylogenetic analysis tools.

This module provides functions for phylogenetic tree construction and analysis, including neighbor-joining algorithms and tree manipulation utilities.

plastro.phylo.neighbor_joining(distance_matrix: DataFrame, outgroup: str | None = None) → TreeNode[source]

Construct phylogenetic tree using neighbor-joining algorithm.

Uses scikit-bio’s robust neighbor-joining implementation to build an unrooted tree from a distance matrix. This is much more reliable than a custom implementation.

Parameters:

distance_matrix (pd.DataFrame) – Symmetric matrix of pairwise distances between leaves. Index and columns should contain leaf names.
outgroup (str, optional) – Name of outgroup leaf for rooting the tree, by default None.

Returns:

Phylogenetic tree constructed using neighbor-joining.

Return type:

ete3.TreeNode

Examples

>>> import numpy as np
>>> import pandas as pd
>>> from plastro import neighbor_joining
>>>
>>> # Create sample distance matrix
>>> cells = ['A', 'B', 'C', 'D']
>>> dists = np.random.rand(4, 4)
>>> dists = (dists + dists.T) / 2  # Make symmetric
>>> np.fill_diagonal(dists, 0)
>>> dist_df = pd.DataFrame(dists, index=cells, columns=cells)
>>>
>>> # Build tree
>>> tree = neighbor_joining(dist_df, outgroup='A')
>>> print(tree.get_ascii())

Notes

This function uses scikit-bio’s neighbor-joining implementation, which is: - Well-tested and robust - O(n³) time complexity - Handles edge cases properly - Produces accurate phylogenetic trees

The result is converted from scikit-bio format to ETE3 format for compatibility with other PLASTRO functions.

Raises:

ImportError – If scikit-bio is not installed.
ValueError – If distance matrix is invalid or outgroup not found.