Works (3)

Updated: July 5th, 2023 14:48

2020 journal article

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability

PLOS ONE, 15(3).

By: F. Mannino n, S. Wisotsky n, S. Pond* & S. Muse n

MeSH headings : Algorithms; Amino Acid Substitution; Evolution, Molecular; Likelihood Functions; Models, Genetic; Mutation Rate; Phylogeny; Sequence Alignment; Sequence Analysis, DNA / methods
TL;DR: It is demonstrated that the variance of this discretized distribution has an upper bound determined solely by the choice of K and the mean of the distribution, which can introduce biases into statistical inference when estimating parameters governing site-to-site variability of substitution rates. (via Semantic Scholar)
Source: Web Of Science
Added: June 15, 2020

2020 journal article

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies


By: S. Pond*, A. Poon*, R. Velazquez*, S. Weaver*, N. Hepler*, B. Murrell*, S. Shank*, B. Magalis* ...

author keywords: evolutionary analysis; natural selection; hypothesis testing; statistical inference; software engineering
MeSH headings : Genetic Techniques; Phylogeny; Software
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. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: March 10, 2020

2020 journal article

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril


By: S. Wisotsky n, S. Pond*, S. Shank* & S. Muse n

author keywords: evolutionary model; synonymous rate variation; codon model; episodic selection
MeSH headings : Animals; Models, Genetic; Phylogeny; Rhodopsin / genetics; Selection, Genetic; Silent Mutation; Vertebrates / genetics
TL;DR: It is found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates and add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: October 19, 2020

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