 The question of which method of phylogenetic inference is best justified is clearly important, but skips over an important step in phylogenetic inference—the construction of a data matrix of characters. Mishler (2005), for one, argues that it is the most important step! Following Winther (2009), we can separate character analysis which results in the construction of a data matrix from phylogenetic analysis which treats the data as input and produces a phylogeny. This first stage of character analysis has been widely discussed in biology (though surely less widely discussed than the second stage). In addition to the voluminous literature on homology, useful collections of work on characters include those edited by Wagner (2000) and Scotland &amp; Pennington (2000).