A python phylogeny tracking module
Project description
phylotrackpy: a python phylogeny tracker
In in silico evolution experiments, we have the luxury of being able to perfectly track the phylogenies of our populations, rather than having to just infer them after the fact. Phylotrackpy is a Python package designed to help you do so as efficiently as possible.
Features
- Ability to prune out taxa that are extinct and have no extant descendants (to keep memory use under control)
- Flexible control of how taxa are defined (e.g. by genotype, by phenotype, by trait, or by something more complex)
- Highly efficient (implemented in C++ under the hood)
- Includes various phylogenetic topology metrics
How to use
There are three main steps in using phylotrackpy:
- Construct a
Systematics
object - Notify the systematics object whenever anything is born
- Notify the systematics object whenever anyything dies
For more detailed instructions, see the documentation
Installation
Phylotrackpy is available through pip:
pip install phylotrackpy
Project details
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