Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the phylogenetic tree. The exact meaning must be shown clearly on a legend accompanying the phylogenetic tree. If such a legend is not present, the branch length is arbitrary, and the reader should not infer any information.

Trees may or may not have a root. The tree is unrooted if the most recent common ancestor of all organisms of interest is unknown. In this case, the depiction of the phylogenetic relationships resembles a snowflake, not a tree. The scientist can root the tree by including an outgroup into the analysis. An outgroup is an organism that is not closely related to any of the organisms that the scientist wishes to arrange on the tree.