Newick Tree Validator and Formatter

Simple utility to validate and format Newick trees.

The main use of this utility is to validate constraint trees used with IQtree2.

IQtree2 can throw hard to understand errors when using constraint trees even if the tree is technically a valid Newick tree.

This utility will catch many of those errors and provide a more detailed error message.

Installation

You can install the utility using pip:

pip install nwkfmt

Usage

Validation without formatting:

./main.py <tree.nwk>

In place formatting:

./main.py <tree.nwk> --inplace

Outputting formatted tree to a separate file:

./main.py <tree.nwk> --outfile <output.nwk>

Outputting list of terminal nodes into a text file:

./main.py <tree.nwk> --terminals <terminals.txt>

Formatting even if validation fails:

./main.py <tree.nwk> --inplace --no-validate

Release

This project uses Poetry for dependency management and packaging.

To build a release, run:

poetry build

To publish a release to PyPI, run:

poetry publish

To publish the release to Github, run:

gh release create 0.4.1 dist/*