Trees can be visualized in various tree windows, and statistics about them presented in tree windows, the List of Trees window, and in charts. The appropriate assumption for most phylogenetic studies is 'soft', but calculations using soft polytomies are extremely difficult, and most Mesquite calculations yield results only with dichotomous trees and those with hard polytomies. Individual trees can be marked as using a specific assumption, thus overriding the default (e.g., by using the Set Polytomy Assumption menu items in the Alter/Transform Tree submenu of the Tree menu of the Tree Window). A change in this default applies to all projects and files. The default interpetation is specified in the Defaults submenu of the File menu. Polytomies in trees are interpreted either as 'soft' (uncertainty in resolution) or 'hard' (simultaneous divergence). for effective population size in population genetics) and color (for display purposes). In addition to length, a branch may have various other attributes such as width (e.g. Mesquite can read, edit and write branch lengths in trees.

Unlike MacClade, Mesquite does not support trees with observed taxa fixed in ancestral position. A tree in Mesqite does not need to contain all of the taxa in the taxa block, and indeed can contain as few as one taxon. Trees may contain polytomies (multifurcations) and also unbranched internal nodes. Mesquite typically treats trees as rooted, although it is possible to de-root trees. (As explained in the page on taxa, 'taxon' here is used as shorthand for 'terminal taxon' or 'OTU'.) In Mesquite, a tree refers to the taxa in a particular taxa block and once created cannot be transfered to refer a different taxa block. Phylogenetic trees represent the branching history of descent linking taxa, whether these taxa are species or genes.

Treefile size