At time passes from a divergence between two species, sequences will naturally vary, and deletions and insertions may make it difficult to align the sequences correctly. For restriction enzyme analysis, gene sequences digested by REs are analyzed via gel electrophoresis. Swofford et al. A phylogenetic tree is a graphical representation of the believed evolutionary relationship between a group of organisms. A cladogram, on the other hand, is a more specific representation that is a result of cladistic analysis based on the similarity and most likely origin of current character traits.
Trees can appear in a variety of formats.
The extant or most recent taxa are represented by the terminal nodes, which are also called the tips, leaves, or external nodes, and appear at the top of the cladogram shown in Figure 2. Internal vertices are referred to as nodes, and represent a bifurcation or multifurcation in the species lineages leading to the terminal nodes. There are many different techniques used to produce phylogenetic trees or cladograms, but for any significant size of taxa, computer programs are generally used. Computer programs are suitable for high throughput analysis of such trees, and frequencly use algorithms to minimize the number of possible trees they will test. A key part of tree generation is analysis of how strong each node on the tree is, since some areas may be more difficult to resolve, given limitations in available data.