Hierarchical Clustering Python Packages

skfolio

Python library for portfolio optimization built on top of scikit-learn

factorlasso

Sparse multi-output factor-model estimation with sign constraints, prior-centered shrinkage, data-driven grouped penalties, and consistent factor covariance assembly

genieclust

Genie: Fast and Robust Hierarchical Clustering

dedupe-hcluster

Hierarchical Clustering Algorithms

cohera

Sheaf and hierarchy algorithms

hipart

Hierarchical divisive clustering algorithm execution, visualization and Interactive visualization.

himalayas

HiMaLAYAS: enrichment-based annotation and visualization of hierarchically clustered matrices

constrained-linkage

Python implementation of a (plug-and-play) constrained linkage function for constrained hierarchical clustering with maximum cluster size, minimum cluster size, must-link, cannot-link and custom constraints, returns SciPy-compatible linkage matrix for subsequent Hierarchical Agglomerative Clustering. Based on HEAT published in Energy and AI (2025)

bhclustering

Bayesian Hierarchical Clustering

graphgrove

A framework for building (and incrementally growing) graph-based data structures used in hierarchical or DAG-structured clustering and nearest neighbor search

topicrankpy

A Python package to get useful information from documents using TopicRank Algorithm.

pyminimax

Python implementation of minimax-linkage hierarchical clustering

pyprotoclust

Python Prototype Clustering: an implementation of minimax linkage for hierarchical clustering

localclustering

Python 3 implementation and documentation of the Hermina-Janos local graph clustering algorithm.

picture-text

Interactive tree-maps with SBERT & Hierarchical Clustering (HAC)

clustviz

Visualization of many Clustering Algorithms, via Notebook or GUI

raccoon-cluster

Multi-scale clustering in Python

aroughcun

Multi-scale clustering in Python