BppSuite Manual 2.2.0

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The Bio++ Program Suite Manual

This is the manual of the Bio++ Program Suite, version 2.2.0.

Copyright © 2007-2014 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.
• Alphabet  Alphabets and genetic codes.
• Sequences  Loading sequences/alignments.
• Tree  Loading trees.
• AlphabetIndex  Setting biochemical properties and distances.
• Process  
• 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. 

Process specification
• Model  
• Non-homogeneity  Specific declaration of non-homogeneous modelling.
• FrequenciesSet  Frequencies
• Rates  Rates across sites
• Linking   

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 

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.

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