The alignment of sequences as a task prior to building phylogenetic trees or as an end in itself to determine conserved and divergent regions is a mainstay in bioinformatics analysis and is amply covered in R and Bioconductor with the ape and DECIPHER packages. We'll look at the extremely straightforward procedures for going from sequence to alignment in this recipe.
Note that there are different techniques for different sequence lengths. In this first recipe, we'll look at how to align some Kbp-length sequences such as those that represent genes and proteins.
