<Li> A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree </Li> <Li> A phylogenetic network is not strictly speaking a tree, but rather a more general graph, or a directed acyclic graph in the case of rooted networks . They are used to overcome some of the limitations inherent to trees . </Li> <P> Phylogenetic trees composed with a nontrivial number of input sequences are constructed using computational phylogenetics methods . Distance - matrix methods such as neighbor - joining or UPGMA, which calculate genetic distance from multiple sequence alignments, are simplest to implement, but do not invoke an evolutionary model . Many sequence alignment methods such as ClustalW also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction . Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the optimality criterion of maximum likelihood, often within a Bayesian Framework, and apply an explicit model of evolution to phylogenetic tree estimation . Identifying the optimal tree using many of these techniques is NP - hard, so heuristic search and optimization methods are used in combination with tree - scoring functions to identify a reasonably good tree that fits the data . </P> <P> Tree - building methods can be assessed on the basis of several criteria: </P>

The main trunk at the bottom of a phylogenetic tree represents