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Aequatus

We present the Aequatus, a web-based tool with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures among differing species or subtypes of a common species. The Aequatus utilises web technologies to provide a fast and intuitive browsing experience over complex comparative data. The Aequatus processes and visualises data directly from the Ensembl Compara and Ensembl Core schema databases by using precalculated genomic alignments from Ensembl Compara and relating them to Ensembl Core to gather genomic feature information, visualising phylogenetic and structural relationships among them via CIGAR strings. Whilst applicable to species with high-quality gold-standard reference genomes such as human or mouse, the Aequatus was designed with large fragmented genome references in mind,  e.g. polyploid plants. The ultimate goal of the Aequatus is to provide a unique and informative way to render and explore complex relationships between genes from various species.

Source Code: https://github.com/TGAC/Aequatus

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Institution: Earlham Institute

TGAC Browser

We present the TGAC Browser with novel rendering, annotation and analysis capabilities designed to overcome the shortcomings in available approaches. TGAC Browser, being a web-based client, utilises JavaScript libraries to provide a fast and intuitive genome browsing experience. We focus on harnessing Internet architectures as well as localised HPC hardware, concentrating on improved, more productive interfaces and analytical capabilities.

  • User-friendly: Live data searching, track modification, and drag and drop selection; actions that are seamlessly powered by modern web browser
  • Responsiveness: Client-side rendering and caching, based on JSON fragments generated by server logic, helps decrease the server load and improves user experience
    • TGAC Browser visualises genomic data in different ways, based on the type and amount of data, which is more informative to the user and memory efficien
  • Analysis Integration: The ability to carry out heavyweight analysis tasks, using tools such as BLAST, via a dedicated extensible daemon
  • Annotation: Users can edit annotations which can be persisted on the server, reloaded, and shared at a later date
  • Off-the-shelf Installation: The only prerequisites are a web application container, such as Jetty or Tomcat, and a standard Ensembl database to host sequence features
  • Extensible: Adaptable modular design to enable interfacing with other databases, e.g. GMOD
  • Data format: TGAC Browser processes and visualises data directly from the Ensembl core schema as well as next-generation sequencing (NGS) data output, i.e. BAM/SAM, BigWig/wig, GFF, and VCF.
  • Manual Annotation: Live editing of Genomics annotations within TGAC Browser, saved with versions and can be reverted, exported in Genomics data format for curator to edit datasets (Under development).

Email: Anil.Thanki@earlham.ac.uk

Source Code: https://github.com/tgac/tgacbrowser

 

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Institution: Earlham Institute

NN-tanglegram

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multigene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method.
We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.

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Institution: Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany; ; Institut des Sciences de l’Evolution Montpellier (ISEM), CNRS UMR 5554, Université Montpellier II, Montpellier, France

ArkMAP

ArkMAP is a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics.

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Institution: University of Edinburgh

BioFabric

BioFabric uses a novel network visualization technique that depicts nodes as one-dimensional horizontal lines arranged in unique rows. This is in distinct contrast to the traditional approach that represents nodes as discrete symbols that behave essentially as zero-dimensional points. BioFabric then depicts each edge in the network using a vertical line assigned to its own unique column, which spans between the source and target rows, i.e. nodes. This method of displaying the network allows a full-scale view to be organized in a rational fashion; interesting network structures, such as sets of nodes with similar connectivity, can be quickly scanned and visually identified in the full network view, even in networks with well over 100,000 edges. This approach means that the network is being represented as a fundamentally linear, sequential entity, where the horizontal scroll bar provides the basic navigation tool for browsing the entire network.

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Institution: Institute for Systems Biology

Dendroscope

The program is a visualization tool for large phylogenetic trees and rooted phylogenetic networks. Now on v3.

The program is open source and installers are available for Windows 10, MacOS X and Linux

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Institution: University of Tubingen

v.3 released.

Variant View

 

Variant View is a visualization tool for analyzing genetic sequence variants.

Variant View is useful to domain experts in several ways: First, it integrates diverse data types previously distributed across input files and external databases. Second, it provides summary metrics that are valuable for sorting genes and identifying candidates for further exploration. Third, it displays rich information about variant type and distribution across a gene. This information is not available in any other visualization tool and is valuable for interpreting the biological impact of variants, which requires human inspection.

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Institution: University of British Columbia

VTK

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. Kitware, whose team created and continues to extend the toolkit, offers professional support and consulting services for VTK. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. VTK has an extensive information visualization framework, has a suite of 3D interaction widgets, supports parallel processing, and integrates with various databases on GUI toolkits such as Qt and Tk.

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Institution: Kitware, Inc.

Jalview

Jalview is a free program for protein and nucleic acid multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.  From Jalview 2.8.2, the Jalview desktop also interfaces with the Chimera molecular visualisation system to provide powerful 3D graphics tightly coupled to Jalview's functions.

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Institution: University of Dundee

StratomeX

 

StratomeX is a tool designed for the discovery and characterization of disease subtypes based on genomic and clinical data of patient cohorts with hundreds of patients. The tool provides an interactive interface that enables analyst to quickly explore complex and heterogeneous datasets. 

Stratomex is part of Caleydo, an open source visual analysis framework targeted at biomolecular data.

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Institution: Harvard

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