Installation

The evotree package can be readily installed via PYPI. An example command is given below.

virtualenv -p=python3 ENV (or python3/python -m venv ENV)
source ENV/bin/activate
pip install evotree

Note that if users want to get the latest update, it's suggested to install from the source because the update on PYPI will be later than here of source. To install from source, the following command can be used.

git clone https://github.com/heche-psb/evotree
cd evotree
virtualenv -p=python3 ENV (or python3 -m venv ENV)
source ENV/bin/activate
pip install -r requirements.txt
pip install .

If there is permission problem in the installation, please try the following command.

pip install -e .

Illustration

Continuous-time birth-death Markov Chain Monte Carlo (MCMC) simulation

evotree simulatepbdmage

This figure shows the gene age distributions under a simple continuous-time birth-death Markov Chain Monte Carlo (MCMC) simulation of 10,000 gene families. Panel a shows the simulation with the duplication and loss rates as 1.5 and 1. Panel b shows the simulation with the duplication and loss rates as 1 and 1. Panel c shows the simulation with the duplication and loss rates as 1 and 1.5.

evotree simulatepbdmagewithwgd

This figure shows the gene age distributions under a simple continuous-time birth-death MCMC simulation of 10,000 gene families with a WGD event aged at 1. The gene duplication and loss rates are both 1. Panel a shows the simulation with the retention rate as 0.8. Panel b shows the simulation with the retention rate as 0.4. Panel c shows the simulation with the retention rate as 0.2.