S
Steven Weaver
Researcher at Temple University
Publications - 17
Citations - 2096
Steven Weaver is an academic researcher from Temple University. The author has contributed to research in topics: Web application & Evolutionary dynamics. The author has an hindex of 11, co-authored 17 publications receiving 1280 citations. Previous affiliations of Steven Weaver include University of California, San Diego.
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Journal ArticleDOI
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.
Steven Weaver,Stephen D. Shank,Stephanie J. Spielman,Michael Li,Spencer V. Muse,Sergei L Kosakovsky Pond +5 more
TL;DR: The release ofDatamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data, and HyPhy Vision, an accompanying JavaScript application for visualizing analysis results.
Journal ArticleDOI
Less is More: an Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
M. D. Smith,Joel O. Wertheim,Steven Weaver,Ben Murrell,Konrad Scheffler,Sergei L. Kosakovsky Pond +5 more
TL;DR: Adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion, delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster.
Journal ArticleDOI
Gene-Wide Identification of Episodic Selection
Ben Murrell,Steven Weaver,M. D. Smith,Joel O. Wertheim,Sasha Murrell,Anthony Aylward,Kemal Eren,Tristan Pollner,Darren P. Martin,Davey M. Smith,Davey M. Smith,Konrad Scheffler,Konrad Scheffler,Sergei L. Kosakovsky Pond +13 more
TL;DR: A new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate, and a computationally inexpensive evidence metric for identifying sites subject to episodicpositive selection on any foreground branches.
Journal ArticleDOI
HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.
Sergei L Kosakovsky Pond,Art F. Y. Poon,Ryan Velazquez,Steven Weaver,N. Lance Hepler,Ben Murrell,Stephen D. Shank,Brittany Rife Magalis,Dave Bouvier,Anton Nekrutenko,Sadie R Wisotsky,Sadie R Wisotsky,Stephanie J. Spielman,Stephanie J. Spielman,Simon D. W. Frost,Simon D. W. Frost,Spencer V. Muse +16 more
TL;DR: The 2.5 release of Hyphy 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 backwards compatible with previous HyPhy releases.
Journal ArticleDOI
HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.
TL;DR: HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections, and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens.