The Bioinformatics group at SCRI is involved in the development of many applications and utilities, 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 as the map below shows.

Flapjack

Still in development, Flapjack is a high performance genotype visualization tool capable of handling very large datasets., where the number of lines and/or markers to be displayed may run into the many thousands - this makes it a very useful tool in genetic analysis.

Flapjack allows the user to quickly navigate around a data set, instantly displaying any selected part of the data at any zoom level. The tool provides a single main view of the data, with several additional sub-views alongside, some of which provide dynamic information depending on where the mouse is over the main data area. Flapjack is fully internationalized, and we currently provide versions that run in English and German.

TOPALi

TOPALi provides a graphical interface to advanced phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis. All of TOPALi's methods can be run on remote, high-performance computing clusters, and many of them can be run in parallel to enhance performance even more. TOPALi is developed by BioSS with assistance from SBRN.

CurlyWhirly

CurlyWhirly is a simple-to-use 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.

Comparative Map Viewer

Still in development, this is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. Currently in prototype form, and implemented in Java 2D and Swing, this tools 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.

TetraploidMap

TetraploidMap 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.