Taxa, Trees, Characters ˇ


Character simulations and randomizations

Mesquite can simulate and randomize characters to build statistical tests. On this page we give an overview of these features. A more in-depth account of simulation of DNA sequence evolution is given separately.


Using results of simulations & randomizations

The simulated or randomized characters 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 reproducable.

Simulations of character evolution

Stochastic models can be used to simulate character evolution along the branches of a phylogenetic tree by selecting Simulated Characters (to generate characters one at a time) or Simulated Matrices on Current Tree (to generate whole matrices, on a current tree in a Tree Window), or Simulated Matrices on Trees (to generate whole matrices, each one on a different tree from a source of trees). These options are available whenever characters or matrices might be called for, for instance when making a chart of characters or matrices.
The following are the character types and models that can be simulated:
To use these simulations, the appropriate character model must be defined in advance, with all of its parameters specified. Two models come built-in: a Jukes-Cantor model for DNA simulations, and a Brownian motion model for continuous variable simulations. If you want any other models, created them using New Character Model in the Characters menu.

Viewing results of simulations

Simulated characters can be used in many calculations, but if you want to visualize directly the results of a simulations you can use the Trace Character History feature available in the Analysis:Tree menu of the Tree Window. By default Trace Character History shows a reconstruction of ancestral states. Thus, if the character is simulated, the states at nodes shown would not be the "true" ancestral states that occurred during the simulation, but rather states inferred from the states given to the terminal taxa by the simulation. However, once Trace Character History is active, its Trace menu has a Character History Source menu item. Choose Simulate Ancestral States and specify the simulation. The states indicated at the nodes will then be the true ancestral states in the simulation. You can set the Seed to make the simulation equivalent to simulations done in other contexts.

Randomizing characters

Existing characters can be randomized as follows: