mattheww95 / baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

baltic

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.

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Installation

Use package manager pip to install baltic:

pip install baltic

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Usage

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)

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Copyright 2016 Gytis Dudas. Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.