4.3 BppAncestor: Bio++ Ancestral Sequence and Rate Reconstruction

The BppAncestor 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).

Specific options are:

input.tree.check_root = {boolean}

Tell if the input tree should be checked regarding to the presence of a root. If set to yes (the default), rooted trees will be unrooted if a homogenous model is used. If not, a rooted tree will be fitted, which can lead to optimization issues in most cases. Use the non default option with care!

asr.method = {none|marginal}

Marginal is the only option for now. If set to "none", only nodes frequencies can be output.

asr.probabilities = {boolean}

Tells if we should output the site specific probabilities in each case.

asr.sample = {boolean}

Tell if we should sample from the posterior distribution instead of using the maximum probability.

asr.sample.number = 10 [[asr.sample=yes]]

Number of sample sequences to output.

asr.add_extant = {boolean}

Should extant (observed) sequences be added to the output sequence file? The sequences added are the ones which are used for the actual calculation. It they contained gaps for instance, and that these have been replaced by the unknown character (N or X for example), then the sequence with unknown characters will be used.

output.sites.file = {{path}|none}

Alignment information log file (site specific rates, probabilities, etc).

output.nodes.file = {{path}|none}

Ancestral nodes information: expected frequencies (prefix exp) (see Galtier & Gouy 1998) and a posteriori probabilities of ancestral states (prefix eb).

output.nodes.add_extant = {boolean}

Tell if leaf nodes should be added to the output file.