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Journal ArticleDOI

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

08 Jul 2016-Nucleic Acids Research (Oxford University Press)-Vol. 44
TL;DR: ITOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format, and its account system has been redesigned to simplify the management of trees in user-defined workspaces and projects.
Abstract: 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. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.

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Citations
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Journal ArticleDOI
TL;DR: The current version of iTOL v4 introduces four new dataset types, together with numerous new features, and is the first tool which supports direct visualization of Qiime 2 trees and associated annotations.
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.

4,233 citations


Cites background from "Interactive tree of life (iTOL) v3:..."

  • ...A complete overview of features added since the last publication (14) can be accessed through iTOL’s version history page (https://itol....

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Journal ArticleDOI
Rudi Appels1, Rudi Appels2, Kellye Eversole, Nils Stein3  +204 moreInstitutions (45)
17 Aug 2018-Science
TL;DR: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

2,118 citations


Cites background from "Interactive tree of life (iTOL) v3:..."

  • ...Supplementary Materials: Materials and Methods Figures S1-S59 Tables S1-S43 External Databases S1-S6 15 References (54-184)...

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  • ...S1 to S59 Tables S1 to S43 References (56–186) Databases S1 to S5 13 December 2017; accepted 11 July 2018 10.1126/science.aar7191 International Wheat Genome Sequencing Consortium (IWGSC), Science 361, eaar7191 (2018) 17 August 2018 13 of 13...

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Journal ArticleDOI
TL;DR: In its 20th year, the SMART analysis results pages have been streamlined again and its information sources have been updated, and the internal full text search engine has been redesigned and updated, resulting in greatly increased search speed.
Abstract: SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 8 contains manually curated models for more than 1300 protein domains, with approximately 100 new models added since our last update article (1). The underlying protein databases were synchronized with UniProt (2), Ensembl (3) and STRING (4), doubling the total number of annotated domains and other protein features to more than 200 million. In its 20th year, the SMART analysis results pages have been streamlined again and its information sources have been updated. SMART's vector based display engine has been extended to all protein schematics in SMART and rewritten to use the latest web technologies. The internal full text search engine has been redesigned and updated, resulting in greatly increased search speed.

1,351 citations


Cites methods from "Interactive tree of life (iTOL) v3:..."

  • ...(B) An example domain architecture analysis result, exported from SMART directly into the interactive Tree Of Life (iTOL) version 3 (21)....

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  • ...The phylogenetic tree export has been completely rewritten and made compatible with the version 3 of the Interactive Tree of Life (iTOL) (21), with which these trees and their associated protein domain datasets can be further annotated (Figure 1B)....

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Journal ArticleDOI
24 Sep 2018
TL;DR: Developments in the BIGSdb software made from publication to June 2018 are described and it is shown how the platform realises microbial population genomics for a wide range of applications.
Abstract: The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera. Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes. Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications. The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation. Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes. There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question. In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.

1,349 citations

Journal ArticleDOI
TL;DR: PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick‐start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
Abstract: Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.

1,144 citations


Cites methods from "Interactive tree of life (iTOL) v3:..."

  • ...…analyses (Degnan & Rosenberg, 2009; Rivera‐Rivera & Montoya‐Burgos, 2016): this software program incorporates and streamlines all steps included in such analyses, from data acquisition to phylogenetic tree annotation (the last step employs the iTOL [Letunic & Bork, 2016] webtool) (Figure 2)....

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References
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Journal ArticleDOI
TL;DR: iTOL is a web-based tool for the display, manipulation and annotation of phylogenetic trees that can be interactively pruned and re-rooted.
Abstract: Summary: Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. Availability: iTOL is available at http://itol.embl.de Contact: [email protected]

2,648 citations


"Interactive tree of life (iTOL) v3:..." refers background or methods in this paper

  • ...Ever since the initial release of iTOL in 2006 (5,15), our primary goal was to offer various ways of annotating phylo-...

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  • ...iTOL (5) was one of the first tools to enable the annotation of trees with various types of additional data....

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Journal ArticleDOI
03 Mar 2006-Science
TL;DR: An automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains is developed, revealing interdomain discrepancies in taxonomic classification and suggesting a thermophilic last universal common ancestor.
Abstract: We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

1,505 citations


"Interactive tree of life (iTOL) v3:..." refers background in this paper

  • ...Tree of Life (15) annotated with various datasets, highlighting several novel features, along with iTOL’s interactive user interface....

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  • ...Ever since the initial release of iTOL in 2006 (5,15), our primary goal was to offer various ways of annotating phylo-...

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  • ...Interactive Tree Of Life (http://itol.embl.de) is a webbased tool for the display, manipulation and annotation of phylogenetic trees....

    [...]

Journal ArticleDOI
TL;DR: Current version of iTOL introduces numerous new features and greatly expands the number of supported data set types.
Abstract: 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.

1,446 citations


"Interactive tree of life (iTOL) v3:..." refers background in this paper

  • ...Like in version 2 (14), iTOL provides most common functions available in any phylogenetic tree viewer....

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Journal ArticleDOI
TL;DR: Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks that provides a number of methods for drawing and comparingRoot phylogenetic networks, and for computing them from rooted trees.
Abstract: Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.].

1,396 citations

Journal ArticleDOI
TL;DR: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.
Abstract: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.

1,014 citations