4 Bio++ Program Suite Reference

This section now details the specific options for each program in the Bio++ Program suite.

• bppml: Bio++ Maximum Likelihood.
• bppseqgen: Bio++ Sequence Generator.
• bppancestor: Bio++ Ancestral Sequences and Rates reconstruction.
• bppmixedlikelihoods: Bio++ Site-Likelihoods Inside Mixed Models.
• bppdist: Bio++ Distance Methods.
• bpppars: Bio++ Maximum Parsimony.
• bppconsense: Bio++ Consensus Trees.
• bppphysamp: Bio++ Phylogenetic Sampler.
• bppreroot: Bio++ Serial Tree Re-rooting.
• bppseqman: Bio++ Sequences Manipulation.
• bppalnscore: Bio++ Alignment Scoring
• bpptreedraw: Bio++ Tree Drawing.