bIOINFORMATICS @WUST

UPGMA

An UPGMA phylogenetic‐tree builder in Python, with support for:

• FASTA or precomputed distance‐matrix input
• Needleman–Wunsch scoring → distance conversion
• UPGMA clustering → Newick output
• Optional dendrogram plotting via Matplotlib
• Editable‐install development with uv

Features

• Flexible input: sequences (FASTA) or raw distance matrix (CSV/TSV/TXT)
• Customizable scoring: match/mismatch/gap parameters
• Clean API: io.py, distance.py, tree.py, upgma.py, viz.py, cli.py
• Console tool: UPGMA entrypoint
• Editable installs: rapid dev iterations via uv pip install -e .

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installation

git clone --recurse-submodules https://github.com/Karo555/UPGMA
--> *
uv virtualenv .venv
source .venv/bin/activate
uv pip install -e .

*package manager

I am using uv as a package manager
Install it by running
curl -LsSf https://astral.sh/uv/install.sh | sh
remeber to restart shell after installation.

usage

Build a tree from fasta
UPGMA UPGMA/data/example1.fasta --mode sequences \ -o UPGMA/output/tree1.nwk \ --output-log UPGMA/output/merges1.csv \ --output-plot UPGMA/output/tree1.png

use precompted matrix
UPGMA UPGMA/data/example_matrix1.csv --mode matrix \ -o tree.nwk \ --output-log merges.csv \ --output-plot tree.png

UPGMA --help for more