A recent paper on a GUI interface introduces SAMMate. As the paper states:
With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files.
You might want to check it out if you have Next Generation Sequencing data in the form of BAM/SAM files. A nice feature I haven’t been able to check is that it will export a ‘wiggle’ file for alignment visualization in the UCSC Genome Browser.