The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Open accessAbstract
HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.
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BEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006650 · Cited by 4,556
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002764 · Cited by 1,811
Self-citationRELAX: Detecting Relaxed Selection in a Phylogenetic Framework
Wertheim, J. O., Murrell, B., Smith, M. D., Kosakovsky Pond, S. L., & Scheffler, K. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu400 · Cited by 778
Self-citationCloud computing for genomic data analysis and collaboration
Langmead, B., & Nellore, A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.113 · Cited by 310 · cited 1×
“…computing infrastructure (Weaver et al. 2018) free of charge to the global Kosakovsky Pond et al. . doi:10.1093/molbev/msz197 MBE community, which can be accessed via an internet browser, with the ultimate goal of democratizing access to scientific computing resources (Langmead and Nellore 2018).”
BackgroundInfluentialThe State of Software for Evolutionary Biology
Darriba, D., Flouri, T., & Stamatakis, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy014 · Cited by 48
Cited by
Martin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · doi:10.1101/2021.02.23.21252268 · Cited by 291
Self-citationCicconardi, F., Milanetti, E., Pinheiro de Castro, E. C., Mazo-Vargas, A., Van Belleghem, S. M., Ruggieri, A. A., Rastas, P., Hanly, J., Evans, E., Jiggins, C. D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41412-5 · Cited by 81
A conserved fertilization complex bridges sperm and egg in vertebrates
Deneke, V. E., Blaha, A., Lu, Y., Suwita, J. P., Draper, J. M., Phan, C. S., Panser, K., Schleiffer, A., Jacob, L., Humer, T., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.035 · Cited by 78
Wheeler, L. C., Walker, J. F., Ng, J., Deanna, R., Dunbar-Wallis, A., Backes, A., Pezzi, P. H., Palchetti, M. V., Robertson, H. M., Monaghan, A., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac044 · Cited by 63
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
Lu, H., Li, F., Yuan, L., Domenzain, I., Yu, R., Wang, H., Li, G., Chen, Y., Ji, B., Kerkhoven, E. J., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110427 · Cited by 44
Metadata
- Authors
- Kosakovsky Pond, S. L., Poon, A. F. Y., Velazquez, R., Weaver, S., Hepler, N. L., Murrell, B., Shank, S. D., Magalis, B. R., Bouvier, D., Nekrutenko, A., Wisotsky, S., Spielman, S. J., Frost, S. D. W., & Muse, S. V.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-08-27
- Volume
- 37
- Issue
- 1
- Pages
- 295-299
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2970147901
- Cited by
- 728
- References
- 6
- FWCI
- 13.32
- Type
- journal article
- Language
- en
- Open access
- green
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- Kosakovsky Pond, S. L., Poon, A. F. Y., Velazquez, R., Weaver, S., Hepler, N. L., Murrell, B., Shank, S. D., Magalis, B. R., Bouvier, D., Nekrutenko, A., Wisotsky, S., Spielman, S. J., Frost, S. D. W., & Muse, S. V. (2020). HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msz197
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