The bioformatica toolkit provides ready-to-run sequence analysis and visualization programs and a Java programming library for developers. It is designed for simplicity, speed, efficiency, and extensibility.
The first release will include library classes for efficient reading of sequences in FASTA format, and basic sequence annotation tools: base frequency, k-mer frequency, unusual motifs, prokaryotic gene-finding, etc.
Status: this project is brand-new. There is code in the repository, but functionality is limited to basic sequence statistics. See the Manual page for usage instructions for all existing tools, and check back frequently.
Current functions include:
An announcement will be made when a full release 1.0 is ready. In the meantime, feel free to experiment with what's there. We strive to keep the JavaDoc up to date and informative. More documentation will be added to the Wiki as we go.
To contribute features requests, ask questions or provide feedback, use the discuss group (see right sidebar.)
To contact the developers, email: vanessa (symbol) fridgebuzz (punctuation) com