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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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