The phruta r package: Increasing access, reproducibility and transparency in phylogenetic analyses

Abstract

Current practices for assembling phylogenetic trees often recur to sequence data stored in GenBank. However, the molecular and taxonomic make-up of sequences deposited in GenBank is generally not very clear. phruta, a newly developed r package, is designed to primarily improve access to genetic data stored in GenBank. Functions in phruta further enable users to assemble single- and multi-gene molecular datasets, and run basic phylogenetic tasks, all within r. The structure of the functions implemented in phruta aim to allow users to assemble simple workflows for particular tasks, which are in turn expected to increase reproducibility of relatively simple phylogenies. To support the use of phruta by researchers in different fields with variable levels of coding expertise, this paper presents the first version of salphycon, a shiny web app that aims to increase access to the fundamental functions in the phruta r package. © 2023 The Author. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society.