Taxa, Trees, Characters ˇ


Tree simulations and randomizations

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.


Using results of simulations & randomizations

The simulated or randomized trees can be used or stored in several ways:
To replicate the results of a simulation or randomization, you can use the Set Seed menu item to set the random number seed used. If you are using the same conditions, including the same seed, the simulations and randomizations should be reproducible. However, in some situations, such as when comparing results from different parameters, leaving simulations reproducible can yield non-independent results. To ensure independence (at the cost of exact reproducibility) you can use the Simulation Repeatable menu item.

Evolutionary Simulations of Trees

Species Trees

We recommend you see the page on diversification for more features related to species tree evolution.

Gene Trees

Random Trees

Randomized Trees


Barraclough, T.G. & S. Nee 2001. Phylogenetics and speciation. TRENDS in Ecology and Evolution. 16:391-399.