• GoFish!. This program (available as a Java applet) allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes. It can also be downloaded, with source code, as a jar file; click here.
• ClusterJudge. Not sure which clustering algorithm to use with your gene expression data? ClusterJudge scores the results from any clustering algorithm, using existing annotation, so you can see which one best groups genes by function.
• Complexpander. A wealth of information is now available on interactions between pairs of proteins. Complexpander uses Bayes' Rule to combine interaction information from several sources to predict protein complexes. Results are generated in both graphical and tabular form. Predicted interaction networks may be exported to several network-analysis tools, for further examination.
• Here's the new, improved ChIPper, a tool for analysis of ChIP² data.
• FuncAssociate. This program takes a list of genes as input and produces a ranked list of the Gene Ontology attributes that the input list is enriched (or depleted) for. To download the source click here.
  A new version of FuncAssociate (still at the beta stage!) is now available. This version supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented.
• SILVER produces visual and numerical output to aid in protein-sequence determination from tandem mass spectrometry. You can access SILVER through a web interface or you can download the Python code for it. The software is free of charge, but you must sign our license agreement.
• BioGraphNet is a common standard and collection of services for sharing distributed network information. We provide tools that enable scientists to make their interaction data available through web-services with a minimum of work. In addition, we serve several network data types, and encourage others to participate, using objects we have registered in BioMOBY's ontology.
• BioTrawler is an example application that builds on the interaction services provided using BioGraphNet to dynamically discover suitable distributed data sources for biological networks, integrate those you select 'just in time', and visualize a graph comprising a user-defined set of genes and their neighbors.
• Query Chem is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program Interface (API). Query Chem makes it possible to search the Web for information about chemical structures without knowing their common names or identifiers. Query Chem's search results can retrieve many interesting structure-property relationships of biomolecules on the Web.

Software in this section has a more utilitarian bias to it. These programs are often not associated with any given project, but some are used silently 'behind the scenes' in several projects. We provide them 'as-is', and while we will be happy to answer short questions, we regret we cannot provide detailed or ongoing support. We welcome comments, suggestions, raves, and chocolate.

• Yorfeus automatically downloads the Saccharomyces Genome Databse (SGD) tables mapping common gene names, ORFs, SGD IDs, and their aliases to each other. It provides an easy command-line interface for looking up information, for human users or other programs. It's always up-to-date. You can download Yorfeus here.
• qqsub is a wrapper to the PBS queuing system, designed to make submitting jobs more convenient. It makes good on several perceived shortcomings of OpenPBS, to make the batch-queuing system as transparent as possible, particularly for novice users.
• Our Synergizer project aims to catalog synonymous identifiers for genes and proteins. synergizer/translate is a a web interface to the Synergizer database that allows users to translate gene names from one naming scheme ("namespace") to another. For more information about the Synergizer, please vist the Synergizer page.