Alignment & Assembly
Specialized BLAST -- Align two (or more) sequences (bl2seq).
For gene sequencing projects, we use the University of Washington (free for academic use) programs: phred, phrap, consed (shown above) and polyphred (SNP calls). The figure below shows a set of aligned reads. It's the industry standard, but takes some system administration expertise to get running.
An easy to install, cross-platform application is ClustalX (gui for clustalw). It is available on-line too. For Unix (and Unix-like, e.g. MacOSX), there are T-Coffee and MAFFT (cross-platform) These are available for use on-line as well.