4.2 BppSeqGen: Bio++ Sequence Simulator

The BppSeqGen program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (see Sequences) and tree (see Tree), specifying the model (see Model) and writing sequence data (see WritingSequences).

number_of_sites = {int>0}

The number of site positions to simulate.

input.infos = {path}

A info file like the one output by bppML. The estimated site-specific rates will then be used to simulate the same number of sites as found in the info file, with the corresponding rates.