Downloading and Installing DendroPy

DendroPy can be installed directly from the Python Package Index using a package manager such as pip or setuptools, or alternatively the source code can be downloaded and manually installed.

Installing from the GitHub Repositories

We recommend that you install directly from the main GitHub repository using pip (which works with an Anaconda environment as well):

$ python3 -m pip install git+https://github.com/jeetsukumaran/DendroPy.git
$ python3 -m pip install git+git://github.com/jeetsukumaran/DendroPy.git

If you already have DendroPy installed, you can upgrade to the latest release version by using the “--upgrade” flag:

$ python3 -m pip install --upgrade git+https://github.com/jeetsukumaran/DendroPy.git
$ python3 -m pip install --upgrade git+git://github.com/jeetsukumaran/DendroPy.git

Note: If you do not have pip installed, you should definitely install it !

Installing From the Python Package Index

DendroPy is also “easy_installable” directly from the Python Package Index:

$ python3 -m pip install -U dendropy

Installing via Conda

$ conda install pip $ pip install dendropy

Source Download and Installation

The latest release of DendroPy (5.0.2), can be downloaded directly from here:

Once downloaded, it can be installed by running:

$ tar -xvzf DendroPy-5.0.2.tar.gz
$ cd DendroPy-5.0.2
$ python3 setup.py install

Installing the Latest Development Version

If you want to install from a particular branch, e.g., the latest development branch, “development-main”, you can use:

$ pip install git+https://github.com/jeetsukumaran/DendroPy.git@development-main

Or:

$ pip install git+git://github.com/jeetsukumaran/DendroPy.git@development-main

And, to update to incorporate changes as they are added to the branch:

$ python3 -m pip install --upgrade git+https://github.com/jeetsukumaran/DendroPy.git@development-main
$ python3 -m pip install --upgrade git+git://github.com/jeetsukumaran/DendroPy.git@development-main

Cloning the Source Code Repository

The DendroPy source code is version-controlled using Git, and the DendroPy Git repository can be cloned by running:

$ git clone git://github.com/jeetsukumaran/DendroPy.git

If you plan to use this repository code as you main library code, you probably want to install DendroPy in developer mode:

$ cd DendroPy
$ python3 -m pip install -e .

You will, of course, need to get yourself Git for the above to work: