IcyTree: rapid browser-based visualization for phylogenetic trees and networks

Alfonso Valencia,Timothy G Vaughan

doi:10.1093/bioinformatics/btx155

Alfonso Valencia, Timothy G Vaughan

Open Access

https://doi.org/10.1093/bioinformatics/btx155

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Journal: Bioinformatics	Publication Date: Apr 12, 2017
Citations: 95	License type: CC BY 4.0

Affiliation: University of Auckland

Abstract

SummaryIcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible.Availability and ImplementationIcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License.

Highlights

The visualization of phylogenetic trees is an extremely important aspect of computational phylogenetics
There exists a range of stand-alone phylogenetic visualization tools, too many to name here. (The PHYLIP home page provides an online list of such programs which currently contains 60 entries.) Despite existing solutions to the visualization problem being so numerous, the package IcyTree distinguishes itself in a number of important respects
Phylogenetic networks specified using the Extended Newick format (Cardona et al, 2008) are supported. (The style used by IcyTree to render such networks is suited to ancestral recombination graphs such as those inferred by Bacter (Vaughan et al, 2017).)

Summary

Introduction

The visualization of phylogenetic trees is an extremely important aspect of computational phylogenetics. Many of the earliest available phylogenetic inference packages such as PHYLIP (Felsenstein, 1989), MacClade (Maddison and Maddison, 1989), and MrBayes (Ronquist et al, 2012) include built-in support for visualizing their output. It is written entirely in JavaScript and runs in modern web browsers (compatibility with recent versions Google Chrome and Mozilla Firefox is assured) without needing additional plugins, meaning that it is loaded by navigating to its home page. And unlike many of the existing JavaScript-based phylogenetics tools, IcyTree does not interact with servers in any way while running This ensures that the program is as responsive as possible and means that users need not be concerned about the privacy implications of uploading data to an online service. Phylogenetic networks specified using the Extended Newick format (Cardona et al, 2008) are supported. (The style used by IcyTree to render such networks is suited to ancestral recombination graphs such as those inferred by Bacter (Vaughan et al, 2017).)

Basic use and capabilities

Supported input formats