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Niema Moshiri edited this page Jul 19, 2024
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TreeSwift is a Python package for efficiently traversing and manipulating ultra-large phylogenetic trees. It should support all versions of Python 3.
TreeSwift can be installed using pip
:
sudo pip install treeswift
If you are using a machine on which you lack administrative powers, TreeSwift can be installed locally using pip
:
pip install --user treeswift
Typical usage should be as follows:
- Import the
treeswift
package - Use
treeswift.read_tree_newick
to load your Newick tree - Use the various
Tree
class functions on the resulting object as you need
import treeswift
tree = treeswift.read_tree_newick(my_newick_string)
for node in tree.traverse_postorder():
print(node)
For more examples, take a look at the Cookbook. Full documentation can be found at: https://niema.net/TreeSwift
Niema Moshiri 2018