https://github.com/broadinstitute/delphy
Fast, scalable, accurate and accessible Bayesian phylogenetics
Science Score: 57.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, ncbi.nlm.nih.gov -
○Academic email domains
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✓Institutional organization owner
Organization broadinstitute has institutional domain (www.broadinstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Repository
Fast, scalable, accurate and accessible Bayesian phylogenetics
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: other
- Language: C++
- Default Branch: main
- Size: 4.29 MB
Statistics
- Stars: 39
- Watchers: 10
- Forks: 4
- Open Issues: 0
- Releases: 17
Metadata Files
README.md
Delphy
Delphy is a fast, scalable, accurate and accessible tool for Bayesian phylogenetics based on Explicit Mutation-Annotated Trees (EMATs). EMATs are an extension of the Mutation-Annotated Trees (MATs) introduced by UShER where nodes have explicit times, mutations are represented as explicit timed events along branches, and missing data is explicitly represented. EMATs open substantial simplifications and scaling opportunities in the calculations powering Bayesian phylogenetics, at the cost of some statistical efficiency with respect to the traditional calculations based on Felsenstein pruning. For genomic epidemiology datasets, where the total number of mutations on a tree is comparable to the number of samples, this is a very favorable trade-off.
These sources comprise the "core" computational engine of Delphy. The web application that allows users to immediately and intuitively use Delphy (currently at https://delphy.fathom.info) is developed in collaboration with Fathom Information Design, and its separately licensed sources are hosted here.
References
Preprint - Delphy: scalable, near-real-time Bayesian phylogenetics for outbreaks. See here for accompanying data and scripts.
Whitepaper with overview of key ideas and accuracy+speed benchmarks
System Requirements
Delphy can be compiled either as a native, standalone command-line program (delphy and its graphical cousin, delphy_ui), or as a WebAssembly bundle that lies at the core of delphy-web. Build instructions for both can be found in INSTALL.md. Delphy does not require special hardware, such as a GPU.
Delphy was developed and is primarily tested under Linux (Ubuntu 22.04.4 LTS and Ubuntu 24.04 LTS, x86-64). Delphy-web, deployed at https://delphy.fathom.info, should work in any modern web browser; see the Delphy-web README.md for specific browsers and operating systems on which it has been tested.
Google Colab Tutorials
Ready-to-use Google Colab tutorials for downloading and formatting sequencing data from the NCBI Virus database, as well as user-provided data, can be accessed here (blank notebook) and here (SARS-CoV-2 example). These notebooks streamline the uniform formatting of sequencing data and the associated metadata for input into Delphy, and then run Delphy using a pre-compiled binary. The output files can be visualized on the Delphy web interface.
Credits and Acknowledgements
Delphy is developed in the Sabeti Lab at the Broad Institute.
Delphy draws a lot of inspiration from:
Copyright (c) 2022-2025 Broad Institute, Inc. See LICENSE for details.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Release event: 1
- Watch event: 12
- Delete event: 4
- Push event: 51
- Pull request event: 3
- Fork event: 1
- Create event: 11
Last Year
- Release event: 1
- Watch event: 12
- Delete event: 4
- Push event: 51
- Pull request event: 3
- Fork event: 1
- Create event: 11
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 10 hours
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- tomkinsc (2)
- lauraluebbert (2)