phyloki 0.5.5

Phyloki

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
• Installation
• Usage Guide
• Contributing
• 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

pip install phyloki

Usage Guide

Demonstrational data is based on the recent paper about identifying novel hantavirus in bats

🔗 Visit 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

Happy tree annotating! 🌳