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Tools and applications

The bioinformatics group at the Institute is involved in the development of many applications, utilities and code libraries, most of which are made freely available for download and use, and several of them are in active use in countries all around the world.

Tablet
Screenshot of Tablet softwareTablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

 

 

Flapjack
Screenshot of Flapjack softwareNew software tools for graphical genotyping and haplotype visualization are required that can routinely handle the large data volumes generated by high throughput SNP and comparable genotyping technologies. Flapjack is a new visualization tool to facilitate analysis of these data types. Its visualizations are rendered in real-time allowing for rapid navigation and comparisons between lines, markers and chromosomes.

CurlyWhirly
Screenshot of CurlyWhirly softwareCurlyWhirly is a very simple Java 3D graph viewer suited for viewing any kind of data in three dimensions. This includes, but is not restricted to, output from Principal Components Analysis or Principal Coordinate Analysis. CurlyWhirly is a Java Swing application and uses the Java 3D API to render its data. It is built using Java 1.6 and is shipped with its own JRE, so there is no need for users to install or update Java.

Strudel
Screenshot of Strudel softwareStrudel is our new 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.

TOPALi
Screenshot of TOPALi softwareThere are a growing number of biological questions that can be answered by analysing multiple sequence alignment data. We have extended the original TOPALi Java application, beyond recombination detection, to launch a range of statistical and evolutionary analyses of multiple sequence alignments as web services. The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.

TetraploidMap
Screenshot of TetraploidMap softwareTetraploidMap is a graphical user interface for calculating linkage maps for autotetraploid populations. It is suitable for handling markers scored on two parents and the full-sib offspring of a cross between them. TetraploidMap handles both codominant and dominant molecular markers, in all possible configurations, and takes into account the presence of null alleles in the analysis. It now includes a routine for QTL mapping. TetraploidMap is developed by BioSS.

Biopython
Biopython LogoThe Biopython Project is an international collaborative effort providing an open source bioinformatics library for the Python programming language. James Hutton Institute staff contributing to Biopython include Peter Cock (core developer) and Leighton Pritchard (GenomeDiagram).

Galaxy
Galaxy ScreenshotThe Galaxy Project is a web-based workflow system for running potentially large or complex bioinformatics analyses from a web browser. Galaxy is an open source project lead by teams at Penn State and Emory Universities in the USA. Contributors from around the world - including here at the James Hutton Institute in Scotland - help to improve the core framework, and write and share additional modular tools via the Galaxy Tool Shed.
 

Research

Areas of Interest


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