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.