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

Note

A detailed example for this tool can be found here

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

breath-helper --help

This tool will create a CSV file with the following columns

Infector, Infectee, Start Date of infection, blockcount, Tree index

To convert the tree distances to dates we need the taxon labels to have date information. The default assumption is that the tip labels are foramted like this:

ID+YYYY-MM-DD
2+2007-11-01

Caution

Use the flags --date-sep and --date-format to specify your layout Be aware that using a separator that is also present in the date format will not work!

If this is not the case the tool will automatically create tip dates. This is done by calibrating the leaf that is furthest from the root to be the current date. If this is required, the tool will also produce a csv dataframe that contains the dates for all taxon labels and all trees in the input.

Important

It is also currently assumed that the float scale is in years, i.e. 1.0 branch length equals 1 year

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.