Regular and extended CCDs

This is a python implementation for conditional clade distributions. This package uses a simple map (dict) based implementation, presented by Larget.

Implemented versions are:

• regular CCD0 and CCD1
• phylogeography CCD1 (assuming fixed leaf labels)
• transmission tree CCD0 and CCD1 using BREATH like trees

Currently, under testing:

• SRanges implementation for sampled ancestors and fossil ranges

Usage

Caution

If you want to use a specific functionality but can not find documentation please let me know.

Phylogeography CCD-MAP tree

The commandline tool for phylogeography trees is called geography and you can use the help to learn more about the input options.

geography --help

Transmission CCD-MAP tree

This package provide a command line interface to compute the tCCD MAP tree. The tool is called transcope and for more information install the package and run

transcope --help

Stratigraphic-range CCD-MAP tree

The command-line tool for computing stratigraphic-range CCD-MAP trees is called fossirange. Use the help command to learn more about the available input options.

fossirange --help

Visualizing the stratigraphic-range CCD graph

The command-line tool fossigraph generates an interactive Cytoscape visualization of the stratigraphic-range CCD graph as an HTML file.

Use the help command to learn more about the available input options.

fossigraph --help

Regular CCD-MAP tree

These can be computed with the tool ccdMAP, use --help to find out how to use it.

Majority rule consensus tree

Use the tool mrc to compute a majority rule consensus tree. This is available for different versions of extended trees, see help.

Breath helper infection date extraction

A commandline tool to extract date information about who-infected-whom. After installation, you can get more information by running

breath-helper --help

There is a GUI wrapper with more details on this tool available at Lars-B/brokilon_transmission_app.

Installation

From GitHub (recommended)

Install the latest version directly from Github:

pip install brokilon@git+https://github.com/Lars-B/pyccd.git

From a release

Alternatively, download the .whl file from the latest GitHub release and install it using:

pip install /path/to/brokilon-<version>-py3-none-any.whl

---

Development install

Clone the repository and install locally:

git clone https://github.com/Lars-B/pyccd.git
cd pyccd
pip install -e .

---

Optional: build manually

If you really want to build the wheel yourself:

python -m build
pip install dist/*.whl

Note that this requires additional packages build and hatchling.