framework, we might encode a set of phenotypes as binary strings (this could be generalized to k-state strings for characters with more than two states) before analyses using an appropriate mode. This can be illustrated using a "toy" example: we can use a binary alphabet to score the following phenotypic traits "has feathers", "lays eggs", "has fur", "is warm-blooded", and "capable of powered flight". In this toy example hummingbirds would have sequence 11011 (most other birds would have the same string), ostriches would have the sequence 11010, cattle (and most other land mammals) would have 00110, and bats would have 00111. The likelihood of a phylogenetic tree can then be calculated using those binary sequences and an appropriate substitution model. The existence of these morphological models make it possible to analyze data matrices with fossil taxa, either using the morphological data alone or a combination of morphological and molecular data (with the latter scored as missing data for the fossil taxa). There is an obvious similarity between use of molecular or phenotypic data in the field of cladistics and analyses of morphological characters using a substitution model. However, there has been a vociferous debate in the systematics community regarding the question of whether or not cladistic analyses should be viewed as "model-free". The field of cladistics (defined in the strictest sense) favor the use of the maximum parsimony criterion for phylogenetic inference. Many cladists reject the position that maximum parsimony is based on a substitution model and (in many cases) they justify the use of parsimony using the philosophy of Karl Popper. However, the existence of "parsimony-equivalent" models (i.e., substitution models that yield the maximum parsimony tree when used for analyses) makes it possible to view parsimony as a substitution model. The molecular clock and the units of time Typically, a branch length of a phylogenetic tree is expressed as the expected number of substitutions per site; if the evolutionary model indicates that each site within an ancestral sequence will typically experience x substitutions by the time it evolves to a particular descendant's sequence then the ancestor and descendant are considered to be separated by branch length x. Sometimes a branch length is measured in terms of geological years. For example, a fossil record may make it possible to determine the number of years between an ancestral species and a descendant species. Because some species evolve at faster rates than