Remarks
Tools using VEGA:
Otter (http://www.sanger.ac.uk/science/tools/otter/) enables human annotators to compare numerous sources of evidence and then to build gene objects with multiple alternative transcripts.
The SeqTools package (http://www.sanger.ac.uk/science/tools/seqtools/) contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu.