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 aspip install Sphinx
basicstrap Html theme for sphinx:pip install recommonmark sphinx-argparse
After required packages are installed, navigate to doc directory, and build the docs by typing:
Instead of html, another target as latex or epub can be specified to build the docs in the desired format.