phyloki
🌳Tool to fetch seqs metadata from NCBI to annotate phylogenetic trees
Science Score: 44.0%
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Low similarity (11.9%) to scientific vocabulary
Keywords
Repository
🌳Tool to fetch seqs metadata from NCBI to annotate phylogenetic trees
Basic Info
- Host: GitHub
- Owner: iliapopov17
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://pypi.org/project/Phyloki/
- Size: 14.3 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
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
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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. ### 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
python
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! 🌳
Owner
- Name: Ilia Popov
- Login: iliapopov17
- Kind: user
- Location: Russia
- Repositories: 1
- Profile: https://github.com/iliapopov17
Citation (CITATION.cff)
cff-version: 0.5.5
message: If you use this software, please cite it as below.
authors:
- family-names: Popov
given-names: Ilia
title: "Phyloki"
date-released: 2024-02-19
url: https://github.com/iliapopov17/phyloki
GitHub Events
Total
- Delete event: 4
- Push event: 1
- Gollum event: 1
- Create event: 5
Last Year
- Delete event: 4
- Push event: 1
- Gollum event: 1
- Create event: 5
Packages
- Total packages: 1
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Total downloads:
- pypi 21 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
pypi.org: phyloki
Annotate phylogenetic trees like never before
- Homepage: https://github.com/iliapopov17/phyloki
- Documentation: https://phyloki.readthedocs.io/
- License: mit
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Latest release: 0.5.52
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- biopython ==1.83
- numpy ==1.26.4
- pandas ==2.2.2
- pytz ==2024.1
- setuptools ==68.2.2
- tzdata ==2024.1
- wheel ==0.41.2