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

Abstract

O_LICurrent 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. C_LIO_LI 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. C_LIO_LIThe 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. C_LIO_LITo 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. C_LI