Welcome to torchtree!#
Warning
The documentation corresponds to the current state of the main branch. There may be differences with the latest released version.
torchtree is a program for inferring phylogenetic trees from molecular sequeces. It is implemented in Python and uses PyTorch to leverage automatic differentiation. Inference algorithms include variational inference, Hamiltonian Monte Carlo, maximum a posteriori and Markov chain Monte Carlo.
Installation#
git clone https://github.com/4ment/torchtree
pip install torchtree/
pip install torchtree
Plug-ins#
torchtree can be easily extended without modifying the code base thanks its modular implementation. Some examples of external packages:
torchtree-bito: is a plug-in interfacing the bito library for fast gradient calculations with BEAGLE.
torchtree-physher: is a plug-in interfacing physher for fast gradient calculations of tree likelihood and coalescent models.
torchtree-scipy: is a plug-in interfacing the SciPy package.
torchtree-tensorflow: is a plug-in interacting with Tensorflow.