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Getting started with TreePPL

We have developed R and Python interfaces to facilitate installation, data preparation, program compilation and execution, post-processing, and visualization of inference results. We strive to provide the same functionalities in R and Python, but there might be small differences between the two interfaces because the project is under active development.

If you want to contribute to TreePPL development, see Instructions for developers.

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We currently support Linux and MacOS only. For Windows users there are two options: use a virtual machine/server/cluster or use TreePPL with WSL (see Windows installation instructions).

For R users​

When you install the R package treepplr, TreePPL and everything it requires is also installed. For that, run within R or RStudio:

Install treepplr from R or RStudio
devtools::install_github("treeppl/treepplr")

treepplr converts data to a format readable by TreePPL, reads the TreePPL output, and connects to downstream analyses in model-specific packages, such as the evolnets package for the host repertoire evolution model.

For complete treepplr documentation, see treepplr. There you will find the complete list of package functions (Reference) and all vignettes (Articles).

For Python users​

To make using TreePPL with Python convenient, you can install the bundled Python package that includes the TreePPL compiler. Follow the steps below to install the package.

Download the prebuilt package​

Download the wheel file treeppl-0.2-py3-none-linux_x86_64.whl.

If you are using Windows, please install the Linux wheel via WSL (Windows Subsystem for Linux).

Install the package​

After downloading the wheel file, open a terminal and navigate to the directory containing it. Then install it using pip:

pip install treeppl-0.2-py3-none-linux_x86_64.whl

Verify the installation​

To confirm the installation was successful, import the package inside a Python session:

import treeppl

If the command run without errors, TreePPL is ready to use.