treesiftr: An R package and server for viewing phylogenetic trees and data

Abstract

treesiftr is a Shiny (Chang, Cheng, Allaire, Xie, & McPherson, 2018) application for visualizing the relationship between phylogenetic trees and the underlying data used to estimate them. It can also be used in RStudio (RStudio Team, 2015) or at the command line as an R package (R Core Team, 2013). treesiftr works by subsetting a phylogenetic matrix according to user-provided input about which characters to visualize. A maximum parsimony tree is then estimated from each data subset. Maximum parsimony was chosen for speed and analytical simplicity. Under the parsimony optimality criterion, the preferred tree is the one that suggests the fewest evolutionary steps, or character changes over evolutionary history. The tree is scored under both parsimony and Lewis’ Mk model (Lewis, 2001), a maximum likelihood model for estimating phylogeny from discrete character data. The data and tree are then visualized using ggtree (Yu, Smith, Zhu, Guan, & Lam, 2017), based upon the ggplot2 (Wickham, 2016) package. Expected outputs are the same whether the learner is interacting via the GUI or the RStudio interface; however, the RStudio interface does have additional options not available in the GUI.