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).

The root sequence can be sampled from the model specification, with additional argument:

number_of_sites = {int>0}

The number of site positions to simulate.

Or the root sequence can be built from a file of a sequence:

input.sequence.file={path}

A sequence is be loaded, from which the simulation will be performed, or from which a root sequence can be sampled. (see Sequences).

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.

In this case, additional options are possible:

input.infos.rates = {string}

Name of the column on which the rates are described (default: pr).

input.infos.states = {string}

Name of the column on which the states are read (default: none, which means a random sequence).

input.site.selection = {string}

used to sample from the given sequence (see Sequences).