Browsing School of Biological and Chemical Sciences by Subject "Bayes Theorem"
Now showing items 1-8 of 8
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Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.
(2014-07)The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the ... -
Bayesian Molecular Clock Dating Using Genome-Scale Datasets.
(2019)Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation ... -
A biologist's guide to Bayesian phylogenetic analysis.
(2017-10)Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and ... -
Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.
(2017-09)Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of ... -
Dating Microbial Evolution with MCMCtree.
(2022)This protocol explains how to use the program MCMCtree to estimate divergence times in microbial phylogenies. The main advantage of MCMCtree is the implementation of an approximation to the molecular data likelihood that ... -
HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.
(2022-09)Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we ... -
Insights into the pleiotropic relationships between chronic back pain and inflammation-related musculoskeletal conditions: rheumatoid arthritis and osteoporotic abnormalities.
(2023-03-01)The ageing process includes the development of debilitating musculoskeletal (MSK) conditions, including chronic back pain (CBP), rheumatoid arthritis (RA), and osteoporosis (OP). The mechanisms involved in the genetic-ep ... -
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.
(2018-07-01)Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the ...