Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees
Zilong He,Zilong He,Huangkai Zhang,Huangkai Zhang,Shenghan Gao,Martin J. Lercher,Wei-Hua Chen,Songnian Hu,Songnian Hu +8 more
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TLDR
Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance.Abstract:
Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.read more
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Journal ArticleDOI
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Ivica Letunic,Peer Bork +1 more
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.
Journal ArticleDOI
GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou,Nabil-Fareed Alikhan,Martin J. Sergeant,Nina Luhmann,Cátia Vaz,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Mark Achtman +8 more
TL;DR: GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
Journal ArticleDOI
Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree.
TL;DR: Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data that can also map and visualize associated external data on phylogenies with two general methods.
Journal ArticleDOI
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.
Balakrishnan Subramanian,Shenghan Gao,Martin J. Lercher,Songnian Hu,Wei-Hua Chen,Wei-Hua Chen +5 more
TL;DR: The new version of Evolview was designed to provide simple tree uploads, manipulation and viewing options with additional annotation types, and the ‘dataset system’ used for visualizing tree information has evolved substantially from the previous version.
Posted ContentDOI
GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou,Nabil-Fareed Alikhan,Martin J. Sergeant,Nina Luhmann,Cátia Vaz,Alexandre P. Francisco,Alexandre P. Francisco,João A. Carriço,Mark Achtman +8 more
TL;DR: G GrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static “GrapeTree Layout” algorithm to render interactive visualisations of large trees.
References
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Journal ArticleDOI
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Ivica Letunic,Peer Bork +1 more
TL;DR: Current version of iTOL introduces numerous new features and greatly expands the number of supported data set types.
Journal ArticleDOI
Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.
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.
Journal ArticleDOI
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
TL;DR: TreeGraph 2, a GUI-based graphical editor for phylogenetic trees, is developed, which allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences.
Journal ArticleDOI
Pathogens and host immunity in the ancient human oral cavity
Christina Warinner,João Domingos Rodrigues,Rounak Vyas,Christian Trachsel,Natallia Shved,Jonas Grossmann,Anita Radini,Y. Hancock,Raul Y. Tito,Sarah Fiddyment,Camilla Speller,Jessica Hendy,Sophy Charlton,Hans U. Luder,Domingo C. Salazar-García,Elisabeth Eppler,Roger Seiler,Lars Hestbjerg Hansen,José Alfredo Samaniego Castruita,Simon Barkow-Oesterreicher,Kai Yik Teoh,Christian D. Kelstrup,Jesper V. Olsen,Paolo Nanni,Toshihisa Kawai,Eske Willerslev,Christian von Mering,Cecil M. Lewis,Matthew J. Collins,M. Thomas P. Gilbert,Frank J Rühli,Enrico Cappellini +31 more
TL;DR: This work reports the first, to their knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrates that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease.
Journal ArticleDOI
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
TL;DR: T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.
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