https://github.com/evogytis/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).
https://github.com/evogytis/baltic
phylogenetics visualisation
Last synced: about 1 month ago
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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).
- Host: GitHub
- URL: https://github.com/evogytis/baltic
- Owner: evogytis
- License: gpl-3.0
- Created: 2016-04-22T20:46:00.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2025-04-25T17:15:27.000Z (about 2 months ago)
- Last Synced: 2025-04-25T17:27:45.893Z (about 2 months ago)
- Topics: phylogenetics, visualisation
- Language: Python
- Homepage: https://phylo-baltic.github.io/baltic-gallery/
- Size: 34.6 MB
- Stars: 101
- Watchers: 10
- Forks: 31
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
[](https://travis-ci.com/evogytis/baltic)
[](https://anaconda.org/bioconda/baltic)
---
### The most recent development version of BALTIC can be found on branch `dev-main`
### For documentation, check out the GitHub [wiki](https://github.com/evogytis/baltic/wiki). For full examples of usage, you can search through the [notebooks](https://github.com/evogytis/baltic/tree/dev-main/docs/notebooks):
- [austechia](https://github.com/evogytis/baltic/blob/dev-main/docs/notebooks/austechia.ipynb): most common BALTIC use cases such as plotting trees, collapsing clades, plotting tanglegrams, etc,
- [curonia](https://github.com/evogytis/baltic/blob/dev-main/docs/notebooks/curonia.ipynb): animations and geospatial integrations,
- [galindia](https://github.com/evogytis/baltic/blob/dev-main/docs/notebooks/galindia.ipynb): integrations with trees generated using the nextstrain toolkit.
### The [BALTIC gallery](https://phylo-baltic.github.io/baltic-gallery/) has several examples of figures generated using BALTIC, and example code for each.
---
# 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.
---
## Installation
Use package manager `pip` to install baltic:
```
pip install baltic
```
---
## Usage
```python
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](https://twitter.com/evogytis). Licensed under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-nc-sa/4.0/).