The ‘phruta’ R package and ‘salphycon’ shiny app: increasing access, reproducibility, and transparency in phylogenetic analyses

Abstract

AbstractCurrent 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’, designed as a workflow, 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 ‘salphycon’, a shiny web app that is expected to increase access to the fundamental functions in the ‘phruta’ ‘R’ package.