A python package containing classes and functions for phylogenetic analyses.
Includes:
- A tree class
- A matrix class
- Functions for reading tree files in newick format
- A function for creating a MRP (supertree) matrix of a set of trees
pip install pylogenetics
import pylogenetics
Read tree files (in newick [default] or tnt format):
trees = pylogenetics.read_trees('/path/to/file.tre')
tnt_trees = pylogenetics.read_trees('/path/to/file.tnt', filetype='tnt')
The read_trees function returns a list of Tree objects (one for each tree in the input file).
The Tree class provides a wrapper around the networkx graph library, with phylogenetic helper methods:
tree = trees[0]
print(tree.tip_names)
tree.drop_tip(name="Tyrannosaurus rex")
tree.drop_tip(key=3)
Trees can be timescaled, using user defined age ranges or ages from the Paleobiology Database
taxon_ages = {'Tyrannosaurus': [70,65], 'Stegosaurus': [155,150], 'Saltasaurus': [70,65]}
tree.timescale(taxon_ages)
This project is licensed under the MIT License - see the LICENSE.txt file for details
White, D.E. (2016) The Evolution and Phylogenetic Analysis of the Dinosaur Axial Skeleton. PhD Dissertation, George Washington University.