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

By Ivica Letunic, Peer Bork. Bioinform., 2007

3,268 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5f312bbe7cd45665b2d0f50b4ac3b5be4e6632a4

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In Molecular Biology

Citations in the corpus

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing (2011, neutral): “The tree was constructed in iTOL (Letunic and Bork, 2007).”
Loss in microbial diversity affects nitrogen cycling in soil (2013, methodology): “Tree plotting with additional OTU abundance data was performed using the iTOL webserver (Letunic and Bork, 2007).”
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, methodology): “Although several software packages are available for the standalone exploration of trees (Letunic and Bork 2007; Huson and Scornavacca 2012; Asnicar et al. 2015) and the programmatic manipulation of data (Paradis et al. 2004; Knight et al. 2007; Sukumaran and Holder 2010; Vos et al. 2011; Talevich…”
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019, methodology): “The visualization of such trees has been covered by various software tools for many years (3,4), including iTOL (5), which introduced the annotation of trees with various types of additional data.”
Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet (2010, methodology): “method and was visualized using the iTOL program (25).”
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, methodology): “Phylogenetics and phylogenetic trees are heavily used in a wide variety of biological and other scientific studies, and classical tree visualization is supported by many software tools (1,2), including Interactive Tree Of Life (iTOL) (3), which introduced the annotation of trees with various types o”
Complementary Function and Integrated Wiring of the Evolutionarily Distinct Drosophila Olfactory Subsystems (2011, methodology): “iTOL (Letunic and Bork, 2007) was used to view and graphically edit the tree.”
Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree. (2018, methodology): “Many software packages and web tools have been developed for visualizing trees in various ways, such as TreeDyn , iTOL (Letunic and Bork 2007), and EvolView (He et al. 2016).”
ETE: a python Environment for Tree Exploration (2010, methodology): “Some well known examples are TreeView [1], a widely used program for inspecting phylogenetic trees; Cluster Treeview [2], an application for visualizing microarray clustering results; ATV [3], a java program used to explore phylogenies which provides also some editing options; MEGA [4], an evolution”
Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding (2012, methodology): “The trees were replotted using the online utility iTOL (Letunic and Bork 2007).”
Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance (2011, methodology): “Dendrogram branches were annotated according to phylum and according to substrate use range using the interactive tree of life (ITOL) web server(3) (Letunic and Bork, 2007).”
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011, methodology): “We have, therefore, developed an in-house tool that included these functions, and made it public after signiﬁcant interest from the small evaluating community (7).”
Ecology of marine Bacteroidetes: a comparative genomics approach (2013, methodology): “The online tool Interactive Tree of Life (Letunic and Bork, 2007, 2011) was used for editing the tree.”
A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data (2008, methodology): “We used iTOL [42] for manual rerooting and visualizing of the trees.”
Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism (2013, background): “Four biopsieswere formalin-fixed and paraffin-embedded for immunohistochemistry; 12 biopsies were placed immediately in 15 ml of RPMI 1640 with 15% fetal calf serum and processed for flow cytometric analysis within 4 hours of collection; two biopsies were placed in RNAlater (Life Technologies) and f”
Understanding and exploiting plant beneficial microbes (2017, methodology): “The tree can be visualized and downloaded on iTOL [101] using the following link: http://itol.”
How Do You Tell a Blackbird from a Crow? (2013, methodology): “Pruning this tree to include only the species in CUBS-200 yields the tree shown in Figure 5 (produced in part with code from [14]).”