Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.

[1]  Emily Jane McTavish,et al.  How and Why to Build a Unified Tree of Life , 2017, BioEssays : news and reviews in molecular, cellular and developmental biology.

[2]  Blair Lawley,et al.  Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package. , 2017, Methods in molecular biology.

[3]  Songnian Hu,et al.  Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees , 2016, Nucleic Acids Res..

[4]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[5]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[6]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[7]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

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

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

[10]  Denis Krompass,et al.  Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood , 2011, Systematic biology.

[11]  E. Virginia Armbrust,et al.  pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree , 2010, BMC Bioinformatics.

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

[13]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[14]  David Swofford,et al.  Inferring Evolutionary Trees with PAUP* , 2003, Current protocols in bioinformatics.

[15]  Sean R. Eddy,et al.  ATV: display and manipulation of annotated phylogenetic , 2001, Bioinform..

[16]  Roderic D. M. Page,et al.  TreeView: an application to display phylogenetic trees on personal computers , 1996, Comput. Appl. Biosci..