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 in development:

• 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 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

tCCD 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

Regular CCD MAP

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 verions 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

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Development install

Clone the repository and install locally:

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

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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.