ATV is a tool for the visualization of annotated phylogenetic trees.
BioJava is an open-source project dedicated to providing Java tools for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. Read more
BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to data synchronization and processing. It automates the update cycle and the supervision of the locally mirrored data repository. The application is generalist, but was applied in the bioinformatics field for biological data bank management. The packaging includes workflow and indexing post-processing scripts for most used biological data banks. Developed in Java and Ant, the application is compatible with various Unix-based systems.
Geneious is an easy-to-use, cross-platform bioinformatics data analysis and visualization tool. It has an open API for writing plugins. You can use Geneious to compare genes from different species, to build an evolutionary tree to see how closely related they are, or to search for literature on any topic in medicine or biology. You can view and extract gene annotations from whole genomes, and interactive 3D graphics allow you to move around protein structures.
JGAP is a genetic algorithms package written in Java. It is designed to require minimum effort to use "out of the box", but is highly modular and allows custom components to be easily plugged in by the more adventurous.
Joone is a free neural net framework to create, train and test neural nets.
PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers.
The Taverna workbench is an open source software tool for designing and executing bioinformatics workflows created by the myGrid project. Read more