Tree simulations and randomizations

[This page is under construction]

Various packages in Mesquite can simulate or randomize trees, allowing you to build statistical tests based on null distributions or trees generated under some hypothesis. Trees so generated can be used directly in charts and the tree window (selecting, for example, Simulate Tree as a tree source), or they can be stored in tree blocks using the "Make New Trees Block From" submenu of the Taxa&Trees menu.

Evolutionary Simulations of Trees

Species Trees

• Uniform speciation (Yule) (trees package) — Generates tree by simple uniform probability speciation (a Yule process) as done by Harding, 1971. The chance of speciation is equal for all tips. Options: total time depth of tree.

Gene Trees

• Coalescent Trees (coalesce package) — Generates tree by coalescence within a single panmictic population. Options: Effective population size.
• Coalescence Contained within Current Tree (coalesce package) — Generates tree by a simple coalescence model of a neutral gene with constant population size, within a current species tree from a Tree window or other tree context. Branch lengths are assigned according to generation of coalescence. The species tree used is a current tree found in a Tree Window or other tree context.

Random Trees

• Equiprobable Trees (trees package)— Generates trees randomly so that each possible labelled tree topology is equally likely.
• Randomly Resolve Polytomies (TreeFarm package) — Randomly resolves polytomies in tree. All possible resolutions are equiprobable. Thus, if the tree is a polytomous bush, the resulting resolved trees will be distributed equivalently to that from the Equiprobable Trees module.

Randomized Trees

• Reshuffle Terminal Taxa (TreeFarm package) — Shuffles (permutes) the taxa among the terminal nodes.
• Add Noise to Branch Lengths (TreeFarm package) — Adds noise to branch lengths of tree. Noise is Normally distributed and proportional to current branch length, except that negative branch lengths are not allowed; changed to zero. Options: variance of noise.
• Add Noise to Divergence Times (TreeFarm package) — Adds noise to branch positions, i.e. divergence times in tree. Noise is Normally distributed and proportional to current branch lengths, except that negative branch lengths are not allowed; changed to zero. Options: variance of noise.
• Rarefy Tree (TreeFarm package) — Rarefies tree by randomly deleting taxa. Options: how many excluded.
• Augment Tree Randomly (TreeFarm package) — Augments tree by random placement of excluded taxa. Options: whether branch lengths are to be considered; whether addition is only to original branches