queeems

Quantify the Extent of Evolutionary Evidence in Molecular Sequences

About

Genetic sequences are only as useful, for evolutionary inferences, as the degree of signatures they retain. When very little time has passed since evolution from the most recent common ancestor, the information accrued in the sequences will most likely be insufficient for any valuable inference to be deducible. When the time since divergence is too long, the sequences are said to have saturated. That is, the evolutionary signatures are most probably significantly eroded for such sequences to yield reliable inferences. Functions designed to assist with quantifying the extent of saturation of genetic sequences are presented. Compared to existing tools for similar purpose, the primary function herein add at least two new features to the literature. First, it is developed upon Bayesian principles. Second, it allows for site-wise assessment of saturation such that it is useful for more than just phylogeny reconstruction inquests. For example, the package is amenable to natural selection pressure analyses.

Contents

• CONTRIBUTING: file where information about how to propose updates or seek assistance when struggling to execute any of the functions within the package.
• DESCRIPTION: file describing the package with more technical details.
• inst: a folder containing a citation file and subfolder(s) where external data used in preparation of the package vignettes, examples and relevant manuscripts are saved.
• LICENSE: a file that contains details of the GNU v3.0 license that governs the free use and sharing of the package
• man: a folder where the R markdown files that contain explanations of how to use each of the functions within the package are saved.
• NAMESPACE: what functions and/or classes are imported and/or exported.
• NEWS: Details of the edits, bug fixes and updates made to the package.
• R: a folder of R scripts that contains different (back-end) functions of the package.
• README: the file that contains the package's preface information.
• tests: a directory of R scripts that contain some test functions. The contents are designed to facilitate internal bug detection.
• vignettes: a folder where the markdown and citation files for building the supporting tutorial document are saved.

Installation

queeems can be installed from Bioconductor with the following code.

if(!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
 BiocManager::install("queeems")