After setting the environment variables on your system, you can run bppML on the provided alignment and tree that way:

./bppML param=optionsFileBppML

You can then use bppAncestor to infer ancestral sequences from the ML estimates produced by bppML:

./bppAncestor param=optionsFileBppAncestor

You can then use bppSeqGen to simulate sequences from the branch ML estimates produced by bppML:

./bppSeqGen param=optionsFileBppSeqGen optionsFileBppML