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      Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

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      Nucleic Acids Research
      Oxford University Press

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          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. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users.

          Graphical Abstract

          Graphical Abstract

          iTOL: an online tool for the tree display and annotation.

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          Most cited references18

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          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.
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            TreeView: an application to display phylogenetic trees on personal computers.

            R D Page (1996)
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              The MEME Suite

              The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression. Since the previous description of the MEME Suite in the 2009 Nucleic Acids Research Web Server Issue, we have added six new tools. Here we describe the capabilities of all the tools within the suite, give advice on their best use and provide several case studies to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses. The MEME Suite is freely available for academic use at http://meme-suite.org, and source code is also available for download and local installation.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                02 July 2021
                22 April 2021
                22 April 2021
                : 49
                : W1
                : W293-W296
                Affiliations
                Biobyte Solutions GmbH , Bothestr 142, 69126 Heidelberg, Germany
                EMBL , Meyerhofstrasse 1, 69117 Heidelberg, Germany
                Department of Bioinformatics, Biocenter, University of Würzburg , 97074 Würzburg, Germany
                Yonsei Frontier Lab (YFL), Yonsei University , Seoul 03722, South Korea
                Author notes
                To whom correspondence should be addressed. Tel: +49 6221 3878534; Email: letunic@ 123456biobyte.de
                Author information
                https://orcid.org/0000-0003-3560-4288
                Article
                gkab301
                10.1093/nar/gkab301
                8265157
                33885785
                dca07353-ded5-4c93-bbc3-d12255611eac
                © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 12 April 2021
                : 29 March 2021
                : 15 February 2021
                Page count
                Pages: 4
                Funding
                Funded by: German Federal Ministry of Education and Research;
                Award ID: 031A537B
                Funded by: European Molecular Biology Laboratory, DOI 10.13039/100013060;
                Categories
                AcademicSubjects/SCI00010
                Web Server Issue

                Genetics
                Genetics

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