https://github.com/uscbiostats/pruner
pruner: Implementing the Felsenstein's Tree Pruning algorithm
https://github.com/uscbiostats/pruner
cpp cpp11 header-only phylogenetic-trees phylogenetics pruning tree
Last synced: 7 months ago
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pruner: Implementing the Felsenstein's Tree Pruning algorithm
- Host: GitHub
- URL: https://github.com/uscbiostats/pruner
- Owner: USCbiostats
- License: mit
- Created: 2019-07-03T19:13:29.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-07-08T23:54:59.000Z (about 5 years ago)
- Last Synced: 2025-01-09T20:42:33.449Z (9 months ago)
- Topics: cpp, cpp11, header-only, phylogenetic-trees, phylogenetics, pruning, tree
- Language: C++
- Homepage: https://uscbiostats.github.io/pruner
- Size: 1.03 MB
- Stars: 1
- Watchers: 1
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
[](https://travis-ci.org/USCbiostats/pruner)
# 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](https://github.com/USCbiostats/pruner/issues) so that we can talk
about it.
Please note that this project is released with a
[Contributor Code of Conduct](https://github.com/USCbiostats/pruner/blob/master/CODE_OF_CONDUCT.md). By participating in this project you agree
to abide by its terms.
## Funding
Supported by National Cancer Institute Grant \#1P01CA196596.