Background Bioinformatics data analysis is usually done sequentially by chaining together multiple tools. These are created by writing scripts and tracking the inputs and outputs of all stages. Writing such scripts require programming skills. Executing multiple pipelines in parallel and keeping track of all the generated files is difficult and error prone. Checking results and task completion requires users to remotely login to their servers and run commands to identify process status. Users would benefit from a web-based tool that allows creation and execution of pipelines remotely. The tool should also keep track of all the files generated and maintain a history of user activities. Results A software tool for building and executing workflows is described here. The individual tools in the workflows can be any command line executable or script. The software has an intuitive mechanism for adding new tools to be used in workflows. It contains a workflow designer where workflows can be creating by visually connecting various components. Workflows are executed by job runners. The outputs and the job history are saved. The tool is web based software tool and all actions can be performed remotely. Conclusions Users without scripting knowledge can utilize the tool to build pipelines for executing tasks. Pipelines can be modeled as workflows that are reusable. BioFlow enables users to easily add new tools to the database. The workflows can be created and executed remotely. A number of parallel jobs can be easily controlled. Distributed execution is possible by running multiple instances of the application. Any number of tasks can be executed and the output will be stored making it is easy to correlate the outputs to the jobs executed.