Phylograms and cladograms are both forms of phylogenetic trees, which differ based on whether the branches are scaled (phylogram) or unscaled (cladogram). These genealogical diagrams are mostly useful tools for hypothesizing and depicting relationships between taxa.
The topology of branches in a tree deﬁnes the relationships between the taxa. The trees can be drawn in different ways, such as a cladogram or a phylogram. In each of these tree representations, the branches of a tree can freely rotate without changing the relationships among the taxa. In a cladogram, however, the external taxa lineup neatly in a row or column. Their branch lengths are not proportional to the number of evolutionary changes and thus have no phylogenetic meaning. In such an unscaled tree, only the topology of the tree matters, which shows the relative ordering of the taxa.
A dendrogram is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of a phylogenetic tree.
A cladogram only represents a branching pattern; such as its branch lengths do not represent time or relative amount of character change, and its internal nodes do not represent ancestors.
A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change.
A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths, a tree whose branch lengths are proportional to time. If the tree we are looking at is ultrametric, that is all branches end flush, and it has a full-length scale bar, we may be dealing with a chronogram. If the scale bar is in units of “Myr” or suchlike and starts with zero in the present we are definitely dealing with a chronogram. Some chronograms may not be ultrametric because they contain extinct species, but the kind of fancy analysis that produces these kinds of trees is still rarely used, not least because many groups don’t have decent fossils available anyway.
A Dahl renogram is a diagram representing a cross section of a phylogenetic tree.
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.
A spindle diagram or bubble diagram, is often called a Romero gram, after its popularization by the American paleontologist Alfred Romer. It represents taxonomic diversity (horizontal width) against geological time (vertical axis) in order to reflect the variation of abundance of many taxa through time. However, a spindle diagram is not an evolutionary tree, the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon and have the disadvantage of involving the paraphyly of the parental group. This type of diagram is no longer used in the form originally proposed. In a rooted tree, the branching indicates evolutionary relationships. The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.
To provide information of tree topology to computer programs without having to draw the tree itself, a special text format known as the Newick format is developed. In this format, trees are represented by taxa included in nested parentheses.