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

By Ivica Letunic, Peer Bork. Nucleic Acids Res., 2019

5,400 citations recorded by the source corpus.

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.

Subfields: Computer Networks and Communications, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fdf4b48dc78b7403d10a2c9681e05fb3f9384a53

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Citations in the corpus

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data (2020, methodology): “Current Protocols in Bioinformatics”
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum (2023, methodology): “The phylogenetic tree was uploaded to iTOL (Letunic and Bork, 2019), where it underwent visual annotation, such as color coding and heatmaps were applied.”
ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data (2021, methodology): “Over the past decade, several packages and web tools have been developed to integrate external data into phylogenetic trees, such as iTOL (Letunic and Bork 2019), Evolview (Subramanian et al.”
SMART: recent updates, new developments and status in 2020 (2020, methodology): “The phylogenetic tree export has been updated and made compatible with the version 5 of the Interactive Tree of Life (iTOL) (15), with which these trees and their associated protein domain datasets are visualized, and can also be further annotated.”
A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. (2020, methodology): “The phylogenetic tree was visualized with iTOL [26].”
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads (2023, positive): “[20, 21], and was visualised in iToL [22].”
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes (2021, positive): “39–41 Additional information was overlaid using IToL templates that are generated through INPHARED.”
DALI and the persistence of protein shape (2019, methodology): “A neighbor-joining tree(32) was generated from the distance matrix (arrow 2) and displayed in iTOL.(33) Domains have the same order in the matrix (bottom-left to top-right) and dendrogram (counter-clockwise).”
A genomic catalog of Earth’s microbiomes (2020, methodology): “The phylogenetic tree was visualized with iTol v5 [19].”
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, background): “A complete overview of changes and functions added since the last publication (14) is listed on the iTOL’s version history page (https://itol.embl.de/version history.cgi).”