Phyloroot

Phyloroot is a python module with tools for orienting undirected phylogenetic networks as oriented networks in several well-known classes.

Install

Install as pypi package phyloroot:

pip install phyloroot

Usage

You can load the package methods with import phyloroot in python, or use the command line interface. For example, to get all orchard orientations of the example network in ./examples/Example1-Components.txt, execute the following command:

phyloroot -f ./examples/Example1-Components.txt -c O

For more information, use the help function:

phyloroot -h

Development

For a development version, simply pull the project and in the home of the project do:

pip install -e .

This installs the phyloroot package from the source. When you change things in the source, the package gets updated as well.

Release

set new version number in master branch

• CHANGELOG.md
• pyproject.toml

release current version

git checkout release
git merge master
git tag [version number]
git push --atomic origin release [version number]