semvec/pypi-packages huggingface dataset:
phyloki 0.5.52
Annotate phylogenetic trees like never before
Requires Python: >=3.10

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> 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)

## 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! 🌳