Mesquite has various tools to simulate and randomize characters and trees, including simulations of DNA sequence evolution, tree reshuffling, coalescent gene tree simulations, and others. With these tools, you can build your own statistical inference methods tailored to your question.

For instance, you can test an hypothesis about phylogenetic structure using parametric bootstrapping, simulating many character matrices on a proposed tree, for each attempting to reconstruct the tree and assessing the reconstruction. Or, you can simulate gene trees within a population to test a population genetics or phylogeographic hypothesis. Or, you can study the effect of branch length uncertainty on calculation of Felsenstein's contrasts by adding random noise to branch lengths on a given tree, repeating many times to see the variation in calculated correlation coefficient of contrasts in two characters. Many other analyses are possible. We give an overview of the features and some examples in the following.

Simulating and randomizing characters

Simulating and randomizing trees, including species trees and gene trees