 Molecular data presents a different set of challenges for individuating characters and coding them into a matrix, nicely illustrated by DNA sequence data. With only four base nucleotides, coding is easy  (§1.2.3),  and modern laboratory techniques provide highly reliable sequences of nucleotides in a stretch of DNA. But here, the problem is alignment. How do we know that one stretch of nucleotide sequences should correspond to similar stretches in other taxa? We might consider chromosomal location, or even functional similarities, though each of these raise other questions of how we decide what ought to be treated as homologous characters (even contingently) across taxa. This becomes even more complicated as we consider how historical processes like gene duplication/loss or recombination add complexity to these questions. This is the problem of positional homology. Like morphological character coding, molecular alignment is intertwined with phylogenetic analysis and various methods of joint inference have been proposed (Redelings &amp; Suchard 2005; Wheeler et al. 2006).