Using simulate

Simulate is used:

1. to generate examples of ``.model'' files for all the substitution models implemented in PHASE . A ``.model'' file is used to provide initial or fixed values for the model parameters to some programs in the package.
2. to generate molecular sequences which evolved from a random initial one according to a specified model of evolution, i.e., phylogeny and substitution model.

To use simulate, type at the command-line:
simulate simulate-control-file
where simulate-control-file is a valid control file for the simulate program. In its first mode of operation simulate create a single ``.model'' file and you can modify this file with your own initial values. In its second mode of operation, simulate displays on screen the tree used to generate the actual sequences. This tree was either provided by the user or randomly created by the program. In the second case the tree is saved in a file specified by the user. Eventually, the likelihood of the generated molecular sequences given the model is printed on the screen and simulate saves the sequences in a file specified by the user. The format of this file is described in the data file format section. If the MIXED model is used, heterogeneous sequences are generated in sequential order.