HyPhy: hypothesis testing using phylogenies
Open accessAbstract
Summary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution. Availability: http://www.hyphy.org Contact: muse@stat.ncsu.edu Supplementary information: HyPhydocumentation and tutorials are available at http://www.hyphy.org
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Controlling for confounding variables such as phylogeny does not reduce statistical power.
“Controlling for confounding variables such as phylogeny does not reduce statistical power, because such variables should be accounted for before making any estimates of power18,114,115.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [115]
The Introduction (page unavailable) describes HyPhy as a platform for likelihood-based analyses of sequence alignments, and §2.1.1 describes model fitting and parameter-estimation variability. Neither addresses whether controlling for phylogeny affects statistical power or whether confounders should be accounted for before estimating power; searches for those points found no supporting passage. (LLM, conf=0.74)
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- Authors
- Pond, S. L. K., Frost, S. D. W., & Muse, S. V.
- Affiliations
- University of California San Diego (US)
- North Carolina State University (US)
- Corresponding author
- Pond, Sergei L. Kosakovsky
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-10-27
- Volume
- 21
- Issue
- 5
- Pages
- 676-679
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2138178197
- Cited by
- 2,866
- References
- 4
- Citations by year
- 2026: 96 · 2025: 101 · 2024: 109 · 2023: 100 · 2022: 131 · 2021: 129 · 2020: 188 · 2019: 173 · 2018: 159 · 2017: 163 · 2016: 195 · 2015: 173 · 2014: 171 · 2013: 176 · 2012: 145
- FWCI
- 17.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (0096033, 9996118)
- National Institutes of Health (AI47745)
- Center for AIDS Research, University of Washington
- National Institute of Allergy and Infectious Diseases (R01AI047745, U01AI043638, P30AI036214)
- Division of Biological Infrastructure
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- HyPhy, phylogeny, hypothesis testing, molecular evolution
- MeSH terms
- Algorithms, Computer Simulation, Models, Genetic, Phylogeny, Software, User-Computer Interface, Sequence Alignment, Evolution, Molecular, Sequence Analysis, Protein
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