How can I generate a pairwise alignment of two sequences?
Look at Bio::Factory::EMBOSS to see how to use the water and needle alignment programs that are part of the EMBOSS suite. Bio::Factory::EMBOSS is part of the bioperl-run package. Or you can use the pSW module for DNA alignments or the dpAlign module for protein alignments. These are part of the bioperl-ext package; download it via Getting BioPerl. You can also use prss34 (part of FASTA package) to assess the significance of a pairwise alignment by shuffling the sequences.
