BppSuite Manual 0.7.0

The Bio++ Program Suite Manual

This is the manual of the Bio++ Program Suite, version 0.7.0.

Copyright © 2007, 2008, 2009, 2010, 2011, 2012 Bio++ development team

• Introduction: Introducing the Bio++ Program Suite and this manual.
• Syntax: A general description of the syntax used to communicate with the programs.
• Common: Common options shared by several programs.
• Reference: The exhaustive list of options available for all programs in the Bio++ Program Suite.

--- The Detailed Node Listing ---

Common options encountered in several programs.

• Sequences: Loading sequences/alignments.
• Tree: Loading trees.
• AlphabetIndex: Setting alphabet indexes.
• Model: Setting up a substitution model.
• Distribution: Setting of the discrete distributions.
• Estimation: Estimating parameters by maximizing a likelihood function.
• WritingSequences: Writing sequences/alignments to files.
• WritingTrees: Writing trees to files.

Model specification

• Declaration: Numerous declarations of models.
• Non-homogeneity: Specific declaration of non-homogeneous modelling.
• FrequenciesSet: Frequencies
• Rates: Rates across sites

Setting up the substitution model

• Nucleotide: Nucleotide models
• Protein: Protein models
• Miscellaneous: Miscellaneous models
• Codon: Codon models
• Multiple: General multiple site models
• Meta: Meta models
• Mixture: Mixture of models
• Linking: Linking parameters

Bio++ Program Suite Reference

• 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.