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. |