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DensiTree
Provides a quick method for qualitative analysis of tree sets. The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in topology and branch lengths show up as highly colored areas, while areas with little agreement show up as webs. This makes it possible to quickly get an impression of properties of the tree set such as well-supported clades, distribution of tMRCA and areas of topological uncertainty. DensiTree has been extended to allow visualisation of meta-data associated with branches such as population size and evolutionary rates. Furthermore, geographic locations of taxa can be shown on a map, making it easy to visually check there is some geographic pattern in a phylogeny. Taxa orderings have a large impact on the layout of the tree set, and advances have been made in finding better orderings resulting in significantly more informative visualisations.
Krona
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Allows hierarchical data to be explored with zoomable pie charts. Krona aims to answer questions regarding the relative abundance of taxa across multiple levels of the hierarchy simultaneously. The software supplements existing metagenomic visualizations by creating clearer depictions of abundance estimates and by enabling in-depth understanding of the underlying classifications. Windows and Mac users can create Krona charts with Microsoft Excel using Krona Excel template.
Taxonomer
An ultrafast web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.
PHYLOViZ
A user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. PHYLOViZ Online was developed to allow users to do these analyses without software installation and to enable easy accessing and sharing of data and analyses results from any Internet enabled computer. PHYLOViZ Online also offers a RESTful API for programmatic access to data and algorithms, allowing it to be seamlessly integrated into any third party web service or software.
TreeViewX
Provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE-PUZZLE, and ClustalX. TreeView generates publication quality trees. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*.
T-REX / Tree and reticulogram REConstruction
A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data.
ALVIS
An open-source platform for the joint explorative analysis of multiple sequence alignments and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures.
DendroPy
A cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines.
Newick Utilities
A suite of UNIX shell programs for processing any number of phylogenetic trees of any size. Newick Utilities performs frequently-used tree operations without requiring user interaction. It allows tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. It has no hard-coded limits, so it can handle large amounts of data. This tool also adds tree-processing capabilities to a shell user’s toolkit.
PhyloDraw
A unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript.
TreeIllustrator
A user-friendly application to visualize and customize phylogenetic trees. TreeIllustrator has a broad range of functions and capabilities, such as dragging of nodes, different tree shapes, zooming and searching capabilities, and support for large trees. It acts as a solution that integrates the specificity of visualizing phylogenetic trees and the customization options of a drawing program. It also contains a simple and effective method that compares a custom tree with the Tree of Life, by detecting incongruence.
PhyloGena
A flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a basic local alignment search tool (BLAST) search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction).
MrEnt
A program for drawing high-quality, printable phylogenetic trees. MrEnt recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. It combines in a single software a large suite of tree manipulation functions (e.g. handling of multiple trees, tree rotation, character mapping, node collapsing, compression of large clades, handling of time scale and error bars for chronograms) with drawing tools typical of standard graphic editors, including handling of graphic elements and images.
Treevolution
A tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users. It is specially suited for chronograms, helping to discuss and confirm hypotheses.
VOE / Visual Omics Explorer
A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the code, or over the internet without any dependency other than distributing the code through a file sharing service. VOE can interactively display genomics, transcriptomics, epigenomics and metagenomics data stored either locally or retrieved from cloud storage services, and runs on both desktop computers and mobile devices.
IcyTree
Allows to visualize a wide variety of phylogenetic trees and networks. IcyTree supports phylogenetic networks (ancestral recombination graphs in particular), and efficiently draws trees that include information such as ancestral locations or trait values. It provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. The tool can be used to view trees represented using the modern PhyloXML and NeXML formats, although support for these formats is currently limited to trees only.
PhyloProfile
Displays, filters and analyzes multi-layered phylogenetic profiles. PhyloProfile can be employed with phylogenetic profiles comprising hundreds of genes and taxa. It offers an overview of the entire data matrix or can serve to visualize only a subset of genes and taxa for a detailed inspection, without the need of modifying the input data. This tool provides several investigation functionalities: profile clustering, gene age estimation, core gene identification and distribution analysis.
T-BAS / Tree-Based Alignment Selector
Visualizes phylogenetic relationships and metadata for Pezizomycotina, downloads alignments for six loci and performs placement of unknowns using either BLAST or phylogeny-based approaches in RAxML. T-BAS has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades; (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments; (iii) User-customizable metadata can be visualized on the tree.
Wasabi
An open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl.
TreeScaper
An application for tree set visualization as well as the identification of distinct phylogenetic signals. TreeScaper allows users to accomplish many different tasks, including (i) computing pairwise distances between trees with a variety of different metrics, (ii) projecting and visualizing trees in low dimensional Euclidean space, (iii) estimating the intrinsic dimensionality of the space formed by the tree set, (iv) computing the covariance matrix of bipartition presence/absence across trees, and (v) finding communities of bipartitions or trees using state-of-the-art community detection methods.
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.
CompPhy
A web-based collaborative platform for comparing phylogenies. CompPhy offers functionalities for tree edition, tree comparison, supertree inference and data management in a collaborative environment. The latter aspect is a specific feature of the platform, allowing people located in different places to work together at the same time on a common project. CompPhy thus proposes shared tree visualization, both synchronous and asynchronous tree manipulation, data exchange/storage, as well as facilities to keep track of the progress of analyses in working sessions.
ETE / Environment for Tree Exploration
A python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations.
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