Detailed Sequences for Trees Unblemished (DSTU) 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.
| The Good 😎 | The Bad 😒 | The Ugly 🚮 |
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DSTU 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.
- Facilitates the retrieval of sequences from NCBI GenBank using specified accession numbers.
- Enhances IQ-TREE constructed trees by replacing accession numbers with the corresponding organism names for clarity and context.
- Gathers host data for each microorganism, including the host's taxonomic order.
- Utilizes the collected host information to prepare detailed annotation datasets, optimizing visualization in iTOL.
I plan to finish all the features of this tool and publish it to
condaoneday!
git clone [email protected]:iliapopov17/dstu.git && cd dstupip install -r requirements.txt- Demonstrational python notebook is available in
demo.ipynbfile - Demonstrational data is available in
demo_datafolder
Demonstrational data is based on the recent paper about identifying novel hantavirus in bats
🔗 Visit DSTU tutorial web page
Contributions are welcome! If you have any ideas, bug fixes, or enhancements, feel free to open an issue or submit a pull request.
For any inquiries or support, feel free to contact me via email
Happy tree constructing! 🌳