CodonCode Aligner  - Our easy-to-use program for assembly, contig editing, and mutation detection for Windows and Mac OS X. Supports base calling with Phred, end clipping, vector trimming, analysis of heterozygous insertions and deletions, and much more. After downloading the free demo version, we suggest you take the quick tour to learn about Aligner's main features.

Phred - Phrap - Consed  - The leading tools for base calling, sequence assembly, and contig editing, developed by Phil Green and coworkers at the University of Washington.

PolyPhred - A tool for SNP detection, especially heterozygous point mutations.

TraceViewer - A Java application to view and edit chromatogram files on Classic Mac OS (on Windows and Mac OS X, the demo version of CodonCode Aligner is a fully functional trace viewer and editor).