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).
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 8 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary
Keywords
Repository
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).
Basic Info
- Host: GitHub
- Owner: evogytis
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Homepage: https://phylo-baltic.github.io/baltic-gallery/
- Size: 34.8 MB
Statistics
- Stars: 107
- Watchers: 10
- Forks: 31
- Open Issues: 13
- Releases: 7
Topics
Metadata Files
README.md
The most recent development version of BALTIC can be found on branch dev-main
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
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. Licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Owner
- Name: Gytis Dudas
- Login: evogytis
- Kind: user
- Location: Vilnius
- Website: https://evogytis.github.io/
- Repositories: 17
- Profile: https://github.com/evogytis
Evolutionary biologist by training, a rogue & a villain by nature; -ssRNA virus geek, matplotlib wizard, Lithuanian.
GitHub Events
Total
- Issues event: 3
- Watch event: 9
- Delete event: 2
- Issue comment event: 2
- Push event: 20
- Pull request event: 3
- Gollum event: 14
- Fork event: 2
- Create event: 3
Last Year
- Issues event: 3
- Watch event: 9
- Delete event: 2
- Issue comment event: 2
- Push event: 20
- Pull request event: 3
- Gollum event: 14
- Fork event: 2
- Create event: 3
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Gytis Dudas | g****s@g****m | 84 |
| gkarthik | x****n@g****m | 21 |
| sidneymbell | s****b@u****u | 9 |
| Trevor Bedford | t****r@b****o | 4 |
| James Hadfield | j****2@s****k | 1 |
| John Huddleston | h****j@g****m | 1 |
| Karthik | k****k@K****l | 1 |
| Sidney Bell | s****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 28
- Total pull requests: 15
- Average time to close issues: 6 months
- Average time to close pull requests: 2 months
- Total issue authors: 16
- Total pull request authors: 5
- Average comments per issue: 1.32
- Average comments per pull request: 0.33
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 3
- Average time to close issues: 35 minutes
- Average time to close pull requests: about 23 hours
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sidneymbell (9)
- colejensen (2)
- andersonbrito (2)
- evogytis (2)
- mattheww95 (1)
- callaband (1)
- sahalpaladan (1)
- batson (1)
- barneypotter24 (1)
- m-a-martin (1)
- staneta (1)
- ViralVerity (1)
- xieduo7 (1)
- MikeWLloyd (1)
- virologist (1)
Pull Request Authors
- barneypotter24 (5)
- gkarthik (4)
- evogytis (4)
- trvrb (1)
- sidneymbell (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 496 last-month
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 13
- Total maintainers: 2
pypi.org: baltic
Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees
- Homepage: https://github.com/evogytis/baltic
- Documentation: https://baltic.readthedocs.io/
- License: gpl-3.0
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Latest release: 0.3.0
published over 1 year ago
Rankings
Maintainers (2)
Dependencies
- matplotlib >=2.0.0
- numpy >=1.16