Each tool has a separate input page with a web form in which the user can input sequence data, upload sequence files, and specify options. All tools that take alignments as input accept the most widely used formats (FASTA, CLUSTAL, Stockholm and A3M). You may also choose your own job-names to organize your work. Snail symbols inside the submit buttons inform you about tools that typically run for more than 10 minutes.

Located on the left of the screen is a sidebar pane that holds a status and section-coded list of all recent jobs in the current session. You can click on previously submitted jobs to check their status and view their results.

In general a session will last until the web browser is closed. However, because of different session implementations by the various browser types, jobs may occasionally disappear from the joblist. Therefore, noting down the job ids is recommended. Anonymous job results are stored two weeks, whereas jobs of logged-in users are stored at least two months.

Most of the tools in the Toolkit are interconnected, allowing job results of one tool to be forwarded as input to others. For example, you could run PSI-BLAST, parse out a multiple alignment of selected hits and send the results to a cluster analysis tool.

You may upload customized databases which are then accessible throughout the whole toolkit (upload once, use many times).