Alignment (making hypotheses of primary homology) and tree searches (testing hypotheses of primary homology) are logically independent steps in phylogenetic analysis. Although both approaches may be incorporated into a single step (Wheeler, 1996), they need not be. Although gaps do not occur in organisms and therefore cannot be directly observed, gaps are as much a part of the pattern of aligned sequences as bases are. Because this aligned pattern is used to code characters for tree searches, the informative variation from gaps should be incorporated along with base characters into tree seaches. We assert that gaps are properly coded as separate presence/absence characters (not as fifth characters states for nucleotides or 21st character states for amino acids) because although gaps are an alternative form of an aligned position (or positions), the do not represent alternative forms of bases. In addition ot evidence that contiguous gap position originate as single indel events, the parsimony criterion favours the interpretation of conding contiguous gap positions as single characters because of the co-occurring pattern. Two methods are proposed by which gaps coded as characters can be implemented in tree seaches. Simple indel coding is easy to implement but does not utilize all available information and can cause ambiguous optimizations of gap characters. Complex indel coding is more difficult to implement but allows all available information to be utilized. Simple and complex indel coding are justified on both theoretical and methodological bases.
