THIS TOOL WILL BE REWRITTEN COMPLETELY TO WORK LOCALLY

Phyloki simplifies phylogenetic tree creation in microbiology and virology by facilitating sequence downloads 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

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.

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

I plan to finish all the features of this tool and publish it to conda oneday!

git clone [email protected]:iliapopov17/phyloki.git && cd phyloki

pip install -r requirements.txt

Usage Guide

• Demonstrational python notebook is available in demo.ipynb file
• Demonstrational data is available in demo_data folder

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 constructing! 🌳