Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

By Ivica Letunic, Peer Bork. Nucleic Acids Res., 2011

1,541 citations recorded by the source corpus.

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/05d14d61c4f0932ba8e7f792f76df11583f13b23

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Citations in the corpus

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes (2015, background): “Accordingly, we observed ten pairs of inversed patterns, in which pathways that (http://phylot.biobyte.de/index.html), and visualized through iTOL (http://itol.embl.de/) (Letunic and Bork, 2007, 2011). were present or absent in one genome were absent or present in another, respectively (Figure 10).”
Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean (2013, methodology): “Categories were mapped on the PhyloAssigner reference tree using the Interactive Tree of Life software (Letunic & Bork 2011).”
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (2014, methodology): “To search for potential contaminants, unaligned scaffold fragments were blasted to the complete reference genome set, and the best hit (with identity and coverage threshold of ≥ 95% and ≥ 80%, respectively) was extracted.”
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data (2011, neutral): “Figure 5 was constructed using iTOL [53].”
Genetic and Genomic Resources of Small Millets (2016, methodology): “1 (Letunic and Bork, 2011) and visualized using online tool EvolView (Zhang et al.”
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.”
Protein Complexes in Bacteria (2015, methodology): “A cladogram of all species in the set was prepared using the Interactive Tree of Life (iTOL, [26]) project as per NCBI taxonomy.”
SMART 7: recent updates to the protein domain annotation resource (2011, methodology): “SMART 7 offers a new data export functions for domain architecture analysis, which is tightly coupled with iTOL [interactive Tree Of Life (10,11)], our phylogenetic tree visualization tool.”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “The recognition that horizontal genetic exchange is widespread among bacteria (Smith et al., 1991) established the necessity of employing multiple loci in characterization schemes, as frequent recombination reassorts loci, consequently breaking down phylogenetic congruence within bacterial genomes…”
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees (2016, background): “Like in version 2 (14), iTOL provides most common functions available in any phylogenetic tree viewer.”
New insights into the ecology of the globally significant uncultured nitrogen-fixing symbiont UCYN-A (2016, methodology): “The ML tree and associated metadata were visualized using the iTOL v2 web platform (Letunic & Bork 2011).”
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees (2012, background): “A wide variety of tree-viewing tools have been developed in the past years, such as TreeView (1), Dendroscope (2), iTol (3), jsPhyloSVG (4), PhyloWidget (5) andmany others (6–16).”
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges (2011, methodology): “Precomputed phylogenetic trees are also provided and can be viewed together with any assigned PFAM (47) and SMART (48) domain via iTOL (49) or downloaded in Newick format.”