We recently released Easy Data Transform. It is a tool for merging, cleaning, reshaping and analyzing tabular data. Itis available for Windows and Mac.
Some customers have been using for it manipulating DNA and protein data and told us it is highly suitable for this task.
It supports multiple input and output formats, including CSV, Excel, JSON and XML, and 42 separate data transformations. It is mostly drag and drop, but you can use regular expressions or Javascript if you need to. There is also a batch processing mode. It is a commercial tool, but very affordable ($99 one-time fee) and fully-functional free trial.
We would welcome feedback on how we can make this tool more useful for bioinformatics applications.