Iroki: automatic customization and visualization of phylogenetic trees.

Ryan M Moore,Sean M Mcallister,Shawn W Polson,K Eric Wommack,Amelia O Harrison

doi:10.7717/peerj.8584

Abstract

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

Highlights

Community and population ecology studies often use phylogenetic trees as a means to assess the diversity and evolutionary history of organisms
Standalone tree visualization packages allowing manual or batch modification of trees are available (e.g., Archaeopteryx (Han and Zmasek, 2009), Dendroscope (Huson et al, 2007), FigTree (Rambaut, 2006), TreeGraph2 (Stöver and Müller, 2010), Treevolution (Santamarıa and Therón, 2009)), but the process can be time consuming and error prone especially when dealing with trees containing many nodes
Iroki is well suited to projects in microbial ecology and those that deal with microbiome data, as these types of studies generally have rich sample-associated metadata and represent complex community structures

Summary

Introduction

Community and population ecology studies often use phylogenetic trees as a means to assess the diversity and evolutionary history of organisms. Some packages allow batch and programmatic customizations through the use of an application programming interface (API) or command line software (e.g., APE (Paradis et al, 2004), Bio::Phylo (Vos et al, 2011), Bio.Phylo (Talevich et al, 2012), ColorTree (Chen and Lercher, 2009), ETE (Huerta-Cepas et al, 2016), GraPhlAn (Asnicar et al, 2015), JPhyloIO (Stöver et al, 2016), phytools (Revell, 2012), treeman (Bennett et al, 2017)). While these packages are powerful, they require substantial computing expertise, which can be an impediment for some scientists

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Conclusion