R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework.

Qiqing Tao, Sudip Sharma, Koichiro Tamura, Sudhir Kumar

Abstract readPreprint

In one paragraph

Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

4 authors.

Qiqing TaoInstitute for Genomics and Evolutionary Medicine, Temple University.

Sudip SharmaInstitute for Genomics and Evolutionary Medicine, Temple University.

Koichiro TamuraDepartment of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.

Sudhir KumarInstitute for Genomics and Evolutionary Medicine, Temple University.

Funding

Methods For Evolutionary Genomics AnalysisR35GM139540 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI Sudhir Kumar · 2021 to 2026

$2.9M

Inferring molecular evolutionary rates and divergence datesR01GM126567 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI KUMAR, SUDHIR · 2018 to 2020

$951k

NIGMS NIH HHS R01 GM126567NIGMS NIH HHS R35 GM139540

6 · The paper itself

Abstract

The relative rate framework (RRF) can estimate divergence times from branch lengths in a phylogeny, which is the theoretical basis of the RelTime method frequently-applied, relaxed clock approach for molecular dating that scales well for large phylogenies. The use of RRF has also enabled the development of computationally efficient and accurate methods for testing the autocorrelation of lineage rates in a phylogeny (CorrTest) and selecting data-driven parameters of the birth-death speciation model (ddBD), which can be used to specify priors in Bayesian molecular dating. We have developed Availability and Implementation: The source codes and related instructions for installing and implementing

Indexed as

Bayesian priordivergence timesRrelative rate framework

Identifiers

PMID39975442

PMCPMC11838771

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.