For documentation, check out the GitHub wiki. For full examples of usage, you can search through the notebooks:
- austechia: most common BALTIC use cases such as plotting trees, collapsing clades, plotting tanglegrams, etc,
- curonia: animations and geospatial integrations,
- galindia: integrations with trees generated using the nextstrain toolkit.
The BALTIC gallery has several examples of figures generated using BALTIC, and example code for each.
baltic is a Python library for parsing phylogenetic trees. It takes newick, Nexus or nextstrain JSON trees and allows you to manipulate, explore and visualise them. baltic stands for Backronymed Adaptable Lightweight Tree Import Code if you like that sort of thing.
Use package manager pip to install baltic:
pip install baltic
import baltic as bt
# When called with a tree string the `make_tree()` function return a baltic tree object:
treeString='((A:1.0,B:2.0):1.0,C:3.0);'
myTree = bt.make_tree(treeString)
# Otherwise you can import trees from newick, nexus or nextstrain JSON files
newickPath='/Users/myUsername/tree.newick'
myTree = bt.loadNewick(newickPath)
nexusPath='/Users/myUsername/tree.nex'
myTree = bt.loadNexus(nexusPath, absoluteTime = False)
nextstrainPath='https://nextstrain.org/charon/getDataset?prefix=/dengue/denv1'
myTree, myMeta = bt.loadJSON(nextstrainPath)Copyright 2016 Gytis Dudas. Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
