Phyloki

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.

Code & full README
Usage Guide

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.