Yabby is a lightweight bioinformatics workbench written in Perl that provides a centralized framework for the management and reuse of program scripts. The specific design goal of Yabby was to allow easy writing of extensions that provide new functionality, and easy integration of capabilities from other software packages. Yabby currently provides about 30 command scripts useful in different bioinformatics applications, including sequence manipulation, processing of standard database files, and processing of the output generated by standard bioinformatics packages such as NCBI BLAST and HMMER.