https://github.com/iliapopov17/phyloki
🌳Tool to fetch seqs metadata from NCBI to annotate phylogenetic trees
https://github.com/iliapopov17/phyloki
phylogenetic-trees tree-annotation visualization
Last synced: 5 months ago
JSON representation
🌳Tool to fetch seqs metadata from NCBI to annotate phylogenetic trees
- Host: GitHub
- URL: https://github.com/iliapopov17/phyloki
- Owner: iliapopov17
- License: mit
- Created: 2024-04-25T17:28:23.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-05-08T13:17:08.000Z (about 1 year ago)
- Last Synced: 2025-09-24T23:16:54.933Z (9 months ago)
- Topics: phylogenetic-trees, tree-annotation, visualization
- Language: Python
- Homepage: https://pypi.org/project/Phyloki/
- Size: 14.3 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
> Phyloki simplifies phylogenetic tree annotation in microbiology and virology by fetching metadata from NCBI GenBank using accession numbers. It also reinstates organism names in trees constructed with IQ-TREE, retrieves host information about microorganisms, and prepares annotation datasets for further visualization in iTOL.
## Table of contents
- [Features](#features)
- [Installation](#installation)
- [Usage Guide](#usage-guide)
- [Contributing](#contributing)
- [Contact](#contact)
|The Good 😎|The Bad 😒|The Ugly 🚮|
|--------|-------|--------|
|
|
|
|
Phyloki allows easy and simple annotation of phylogenetic trees. See the examples above:
- The best tree contains information about the hosts from which the virus was isolated and the full names of the viruses.
- The so-so tree contains the same information, but is colour annotated with randomly generated colours.
- The worst tree contains only accession numbers on its leaves.
## Features
### Sequence Downloading
- Facilitates the retrieval of sequences from NCBI GenBank using specified accession numbers.
### Metadata Fetching
- Downloads metadata from NCBI GenBank (Accession Number; Organism Name; Country; Year; Host)
### Organism Name Reintegration
- Enhances IQ-TREE constructed trees by replacing accession numbers with the corresponding organism names for clarity and context.
### Host Information Retrieval
- Gathers host data for each microorganism, including the host's taxonomic order.
### Annotation Dataset Preparation for iTOL
- Utilizes the collected host information to prepare detailed annotation datasets, optimizing visualization in iTOL.
## Installation
```python
pip install phyloki
```
## Usage Guide
Demonstrational data is based on the recent paper about identifying novel hantavirus in bats
🔗 Visit [Phyloki wiki](https://github.com/iliapopov17/phyloki/wiki) page
## Contributing
Contributions are welcome! If you have any ideas, bug fixes, or enhancements, feel free to open an issue or submit a pull request.
## Contact
For any inquiries or support, feel free to contact me via [email](mailto:iljapopov17@gmail.com)
Happy tree annotating! 🌳