Actively maintained

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.

GenotypeChecker is a desktop software tool for assisting data cleansing. The application identifies likely data errors in pedigree/genotype data sets by performing an inheritance-checking algorithm for each marker across the pedigree, and highlights inconsistently inherited genotypes in an exploratory user interface. By ‘masking’ suspect datapoints and rechecking inheritance consistency, erroneous datapoints can be confirmed and cleansed from the data set. The software, examples and documentation are freely available at http://bioinformatics.roslin.ac.uk/genotypechecker.

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

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.

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.

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

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.

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.

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.

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.

Features:

• 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