4.6 BppPars: Bio++ Maximum Parsimony

The BppPars program is currently quite limited and should not be used for serious phylogenetic analysis. It can compute parsimony scores and perform topology estimation using the same algorithm of BppML. It uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (see Sequences) and tree (see Tree)).

Specific options are:

optimization.topology = {boolean}

Tell if topology has to be estimated.

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

Where to print the output file.

bootstrap.number = {int>0}

Number of bootstrap replicates to perform.

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

Where to write bootstrap trees.