Links

Trace Viewers

Finch TV - Free trace viewer.

ABI Sequence Scanner - Free trace viewer.  Allows you to look at ABI chromatagrams and raw signals.  Helpful for troubleshooting.  Only works for Windows.

4Peaks -  Free trace viewer for MacOSX platforms. 

Primer Design

Primer3 - Tool that helps you design primers automatically.

ExonPrimer - Automatically designs primers around your exons.  Input reference sequence and cDNA sequence and the program outputs primers that flank the exons.

Tm Calculator - Automatically calculates the melting temperature of your primers.