WebMol analyzes molecular structure information. This program uses Java3D to allow researchers to visualize and manipulate complex protein structures.

Apollo is a genome annotation tool designed for biologists and bioinformaticians. It has been designed to aid in the annotation of genes in various genomes, and has been used to annotate the fruitfly genome and parts of the human genome. Apollo is a good example of a Java bioinformatics tool that integrates biological data to aid in human-facilitated annotation activities.

Sockeye facilitates comparative genome analysis (the science of comparing genomic-level similarities across species). It allows users to view and compare annotation and sequence from several genomes simultaneously. Sockeye uses Java3D to display genomes and their respective annotations (screenshots).

Spice is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

BioJava is more of an API than an application. Many bioinformatics projects exist for different languages. These APIs try to organize the semantics of working with and manipulating biological data. Here a BioJavaAPI PowerPoint presentation, and a complete BioJava CookBook