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Tool is being activelty miantained. This tool is considered complete. Bugs will be fixed, but no new features will be added 

Flapjack

Summary: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features

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Institution: The James Hutton Institute

MizBee

MizBee is a multiscale synteny browser with the unique property of providing interactive side-by-side views of the data across the range of scales supporting exploration of all of these relationship types.

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Institution: School of Computing, University of Utah

PhyloDet

    PhyloDet is a scalable tree visualization that enables biologists to visualize multiple traits or attributes mapped to large evolutionary trees with thousands of leaf nodes representing the species. It also preserves branch lengths that indicate the genetic similarity between two species. PhyloDet is interactive, enabling users to set any node of the tree as the root and to show or hide any branches without re-layout of the tree. PhyloDet enables biologists to visualize complex interactions and how they relate to the evolutionary history of the species.
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Institution: Yonsei University, Seoul, Korea

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

BirdVis

Birds are unrivaled windows into biotic processes at all levels and are proven indicators of ecological well-being. Understanding the determinants of species distributions and their dynamics is an important aspect of ecology and is critical for conservation and management. Through crowdsourcing, since 2002, the eBird project has been collecting bird observation records. These observations, together with local-scale environmental covariates such as climate, habitat, and vegetation phenology have been a valuable resource for a global community of educators, land managers, ornithologists, and conservation biologists. By associating environmental inputs with observed patterns of bird occurrence, predictive models have been developed that provide a statistical framework to harness available data for predicting species distributions and making inferences about species-habitat associations. Understanding these models, however, is challenging because they require scientists to quantify and compare multiscale spatialtemporal patterns. A large series of coordinated or sequential plots must be generated, individually programmed, and manually composed for analysis. This hampers the exploration and is a barrier to making the cross-species comparisons that are essential for coordinating conservation and extracting important ecological information. To address these limitations, as part of a collaboration among computer scientists, statisticians, biologists and ornithologists, we have developed BirdVis, an interactive visualization system that supports the analysis of spatio-temporal bird distribution models. BirdVis leverages visualization techniques and uses them in a novel way to better assist users in the exploration of interdependencies among model parameters. Furthermore, the system allows for comparative visualization through coordinated views, providing an intuitive interface to identify relevant correlations and patterns. We justify our design decisions and present case s- udies that show how BirdVis has helped scientists obtain new evidence for existing hypotheses, as well as formulate new hypotheses in their domain.

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Institution: Cornell Lab of Ornithology; New York University

GeneaQuilts

GeneaQuilts is a new visualization technique for representing large genealogies of up to several thousand individuals. Thevisualization takes the form of a diagonally-filled matrix, where rows are individuals and columns are nuclear families. This is an interactive genealogy explorationsystem based on GeneaQuilts. The system includes an overview, a timeline, search and filtering components, and a new interactiontechnique called Bring & Slide that allows fluid navigation in very large genealogies.

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Institution: University of Paris South

Strudel

Strudel is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes. All browsing and interaction with Strudel happens in real-time – there is no need to wait while the maps are generated.

Strudel is built using Java 1.6 and ships with its own JRE, so there is no need for users to install or update Java.

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  • Visualize multiple genomes and thousands of homologies interactively and in real time
  • Continuous zoom ranging from entire genome views to singles features
  • Explore intervals such as QTLs and list annotation for features
  • Search for features by name
  • Filter homologies on display by BLAST e-value
  • Single genome mode also supported
  • Ships with example dataset to facilitate familiarization with the software
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Institution: The James Hutton Institute, Dundee University

HerbariaViz

HerbariaViz is a web mapping application that provides space–time–species data query responses efficiently. The open-source methods for aggregating point data spatially and temporally, outline our approach to sound cartographic representations of those data, and detail the design of a client interface for making requests and mapping responses. A focus group session involving domain experts was performed to provide user evaluation of the application. In our discussion, we present potential avenues of future work, including: facilitating query response comparisons, handling incomplete and inaccurate data, and generalizing the method presented.

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Institution: GeoVISTA Center, Penn State University

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.

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