pruner: Implementing the Felsenstein's Tree Pruning algorithm

This C++ template library provides classes to implement Felsenstein tree-pruning algorithm for efficiently computing likelihood functions on phylogenies.

The library reads in a tree object in the form of std::vector< unsigned int > specifying the source and target of each dyad (edge) and allows the user to store arbitrary arguments using memory pointers, and std::function to be called with those arbitrary arguments and tree structure data.

Trees are stored as two lists: each nodes' offspring, and each nodes' parents, which can be accessed at any point using TreeIterator class that implements tree traversals (pre and post order for pruning).

Contributing

We welcome contributions to pruner. Whether it is reporting a bug, starting a discussion by asking a question, or proposing/requesting a new feature, please go by creating a new issue here so that we can talk about it.

Please note that this project is released with a https://github.com/USCbiostats/pruner/blob/master/CODE_OF_CONDUCT.md "Contributor Code of Conduct". By participating in this project you agree to abide by its terms.

Funding

Supported by National Cancer Institute Grant #1P01CA196596.