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

Abstract Summary IcyTree 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 Implementation IcyTree 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.

[1]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[2]  Alexei J. Drummond,et al.  A Stochastic Simulator of Birth–Death Master Equations with Application to Phylodynamics , 2013, Molecular biology and evolution.

[3]  D. Maddison,et al.  Interactive analysis of phylogeny and character evolution using the computer program MacClade. , 1989, Folia primatologica; international journal of primatology.

[4]  Maxim Teslenko,et al.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space , 2012, Systematic biology.

[5]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[6]  D. Huson,et al.  Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. , 2012, Systematic biology.

[7]  Christian M. Zmasek,et al.  phyloXML: XML for evolutionary biology and comparative genomics , 2009, BMC Bioinformatics.

[8]  Gabriel Cardona,et al.  Extended Newick: it is time for a standard representation of phylogenetic networks , 2008, BMC Bioinformatics.

[9]  D. Maddison,et al.  NEXUS: an extensible file format for systematic information. , 1997, Systematic biology.

[10]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[11]  A. Drummond,et al.  Inferring Ancestral Recombination Graphs from Bacterial Genomic Data , 2016, Genetics.

[12]  Hilmar Lapp,et al.  NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata , 2012, Systematic biology.