Free

Molecular Maya (mMaya) is a free plugin for Autodesk Maya that lets users import, model and animate molecular structures. We leverage the power and flexibility of Maya while offering innovative, intuitive tools specialized for the challenges of molecular modeling and animation. mMaya is further enhanced by a series of 'kits' that expand its functionality and greatly streamline molecular modeling, animation, and simulation.

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is a fast, flexible, and free desktop genome browser. First developed at Affymetrix in 2001 to support visual analytics of genome tiling arrays, IGB provides an advanced, highly customizable environment for exploring and analyzing large-scale genomic data sets.

Using IGB, you can:

• View your RNA-Seq, ChIP-chip or ChIP-seq data alongside genome annotations and sequence.
• Investigate alternative splicing, regulation of gene expression, epigenetic modifications of DNA, and other genome-scale questions.
• View results from aligning short-read sequences onto a target genome, identify SNPs, and check alignment quality.
• Copy and paste genomic sequences for further analysis into other tools, such as primer design and promoter analysis tools.
• Create high-quality images for publication in a variety of formats.

IGB features

IGB lets you view results from your own experiments or computational analyses alongside public domain gene annotations, sequences, and genomic data sets, thus making it easier for you to determine how your experiments agree or disagree with current thinking and models of genomic structure.

Some features IGB offers include:

• Animated zooming. Most genome browsers implement "jump zooming" only, in which you click a zoom button (or other type of control) and then wait for the display to re-draw. In IGB, zooming is animated, allowing you to easily and quickly adjust the zoom level as needed without losing track of your location.
• Simple Data Sharing System - QuickLoad. IGB implements a very simple, easy-to-use system for sharing data called QuickLoad. You can use the QuickLoad system to set up a Web site you can use to share your data with colleagues, reviewers, and the public.
• Draggable graphs. You can display genome graphs data (e.g., "bar" and "wiggle" files) alongside and even on top of reference genome annotations, thus making it easier to see how your experimental results match up to the published reference genome annotations. You can reset your graphs to "floating" and click-drag them over annotations to compare your results with annotations and others' experiments.
• Edge-matching across tracks. When you click an item in the display, the edges of other items in the same or different tracks with identical boundaries light up, highlighting interesting similarities or differences across gene models, sequence reads, or other features.
• Integration with local and remote external data sources. IGB can load data from a variety of sources, including Distributed Annotation Servers, QuickLoad servers, ordinary Web sites, and local files.
• Intron-trimming sliced view. In many species, introns are huge when compared to the exonic (coding) regions of genes. IGB provides a Sliced View tab that trims uninformative regions from introns.
• Web-controls. IGB can be controlled from a web browser or any other program capable of sending HTTP requests. Via IGB links, you can create Web pages that direct IGB to scroll to a specific region and load data sets from local files or servers.
• Scripting. IGB understands a simple command language that allows users to write simple scripts directing IGB to show a genome, zoom and scroll to specific regions, and other functions.
• Open source. All development on IGB proceeds via a 100% open source model. The license allows developers to incorporate IGB (and its components) into new applications.

Sequence Bundles is a new tool for visualising and exploring sequence motifs in multiple sequence alignment (MSA) data.

It enables the discovery of data features that would otherwise remain hidden.

In Sequence Bundles, MSA sequences are visualised as continuous strings of data, which helps in preserving and exposing important residue correlations.

Use Sequence Bundles web tool to easily look at your own MSA data in a completely new way.

Vaa3D(in Chinese ‘挖三维’) is an Open Source visualization and analysis software suite created mainly by Hanchuan Peng and his team at Janelia Research Campus, HHMI and Allen Institute for Brain Science. The software performs 3D, 4D and 5D rendering and analysis of very large image data sets, especially those generated using various modern microscopy methods, and associated 3D surface objects. This software has been used in several large neuroscience initiatives and a number of applications in other domains. It has been viewed as one of the leading Open Source software suites in the related research fields. It has also been used in several other award-winning work, e.g. mapping of dragonfly neurons and large-scale visualization of cellular data.

ViPhy supports comparison of multiple phylogenetic trees. It relies on a set of interactive views comparing phylogenetic trees on various detail levels. The views incorporate information on similarity scores and allow highlighting of similar structures in multiple trees. They thereby reveal global and local tree similarities.

Video: http://www.gris.tu-darmstadt.de/research/vissearch/projects/ViPhy/Intera...
Program Files: ViPhy.zip || Version 1.3.1 (16.02.2014)

From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 130 image file formats supported, including all major microscope formats.

Web-based sequence logo viewer

Developed for the BioVis 2012 Redesign Contest, this tool provides a sequence logo using glyph-based approaches to aid interpretation.

This can be deployed using an easy to use JavaScript library that uses Raphael.js to render visualization of one or more sequence logos.

It supports DNA, RNA, and amino acid sequences.

Cite this work

E. Maguire, P. Rocca-Serra, S.-A. Sansone, and M. Chen, Redesigning the sequence logo with glyph-based approaches to aid interpretation, In Proceedings of EuroVis 2014, Short Paper (2014)

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

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

SequenceJuxtaposer is a flexible sequence visualization tool used to explore a set of sequences. It provides an immediate view of a set of sequences that a user can navigate through with a few clicks of a mouse.

SequenceJuxtaposer is a tool for the exploration and comparison of biomolecular sequences. We use an information visualization technique called "accordion drawing'' that guarantees three key properties: context, visibility, and frame rate. We provide context through the navigation metaphor of a rubber sheet that can be smoothly stretched to show more details in the areas of focus, while the surrounding regions of context are correspondingly shrunk. Landmarks, such as user specified motifs or differences between aligned base pairs across multiple sequences, are guaranteed to be visible even if located in the shrunken areas of context. Our graphics infrastructure for progressive rendering provides immediate responsiveness to user interaction by guaranteeing that we redraw the scene at a target frame rate. Our preprocessing algorithms are subquadratic: O(nk) for k sequences of n base pairs each. All runtime rendering algorithms are sublinear in nk: they are O(v) where v is the number of items visible onscreen at once, and v \ll nk. SequenceJuxtaposer supports interaction at 20 frames per second when browsing collections of several hundred sequences that comprise over 1.7 million total base pairs. 

Any FASTA file (DNA or RNA) can be loaded into SequenceJuxtaposer.