Illustration of parsimony inference from a gene/presence pattern and a reference tree topology. (a,b) Results of parsimonious inferences for the same gene family, with different criteria used to define presence/absence patterns. In (a) genes are divided into only two categories, present and absent, while in (b) the absent genes are further classified into gene remnants and genuinely absent.
Zhaxybayeva et al. Genome Biology 2007 8:402 doi:10.1186/gb-2007-8-2-402