Phylogenetic Tree Pruner

This repository contains scripts for pruning parsimony-based phylogenetic trees encoded in Protocol Buffer format. It enables the removal of internal nodes with fewer than a specified number of descendant observations and exports the pruned trees in binary or text format.

Features

• Prune internal nodes based on a minimum observation count (k).
• Support for Protocol Buffer binary and text formats.
• Auto-generated Protocol Buffer message definitions.

Files

• pruner.py: Command-line script to prune a tree in binary Protobuf format.
• ppruner.py: Command-line script to prune a tree and export using Protobuf text format.
• p2.py: Experimental/alternate implementation of the pruning logic.
• parsimony_pb2.py: Auto-generated Protobuf Python classes (data, mut, mutation_list) from parsimony.proto.

Requirements

• Python 3.6 or above

• Packages:

  • bte (for MATree operations)
  • protobuf (for parsimony_pb2.py)
  • Standard libraries: argparse, gzip

Install dependencies:

pip install protobuf bte

Usage

pruner.py

Prune a binary Protocol Buffer tree:

python pruner.py <input_tree.pb> <k> <output_tree.pb>

• <input_tree.pb>: Path to the input tree in binary Protobuf format.
• <k>: Minimum number of descendant observations to retain internal nodes.
• <output_tree.pb>: Path to write the pruned tree.

ppruner.py

Prune and export using Protobuf text format:

python ppruner.py <input_tree.pb> <k> <output_tree.pb>

Arguments are the same as for pruner.py.

p2.py

Alternate pruning version:

python p2.py <input_tree.pb> <k> <output_tree.pb>

Development

• If you modify the Protobuf schema (parsimony.proto), regenerate the Python classes:

  protoc --python_out=. parsimony.proto

• Integrate these scripts into your phylogenetic analysis pipelines as needed.