Installation

TreeTime is compatible with Python 2.7 upwards and is tested on 2.7, 3.5, and 3.6. It depends on several Python libraries:

  • numpy, scipy, pandas: for all kind of mathematical operations as matrix operations, numerical integration, interpolation, minimization, etc.

  • BioPython: for parsing multiple sequence alignments and phylogenetic trees

  • matplotlib: optional dependency for plotting

Installing from PyPi or Conda

You can also install TreeTime from PyPi via

pip install phylo-treetime

You might need root privileges for system wide installation. Similarly, you can install from conda using

conda install -c bioconda treetime

Installing from source

Clone or download the source code.

git clone https://github.com/neherlab/treetime.git
cd treetime
pip install .

You might need root privileges for system wide installation. Alternatively, you can simply use it TreeTime locally without installation. In this case, just download and unpack it, and then add the TreeTime folder to your $PYTHONPATH.

Building the documentation

The API documentation for the TreeTime package is generated created with Sphinx. The source code for the documentaiton is located in doc folder.

  • sphinx-build to generate static html pages from source. Installed as

pip install Sphinx

  • basicstrap Html theme for sphinx:

pip install recommonmark sphinx-argparse sphinx_rtd_theme

After required packages are installed, navigate to doc directory, and build the docs by typing:

make html

Instead of html, another target as latex or epub can be specified to build the docs in the desired format.