bpp Namespace Reference

Classes
class	AbstractDistanceEstimationMafIterator
	Partial implementation for distance estimation iterator. More...
class	AbstractPhylogenyReconstructionMafIterator
	Partial implementation for phylogeny reconstruction iterator. More...
class	CountClustersMafStatistics
	Count the number of sequence cluster, given a certain threshold. This requires that a phylogenetic tree was previously computed. More...
class	CountDistanceEstimationMafIterator
	Compute A simple distance using observed counts. More...
class	DistanceBasedPhylogenyReconstructionMafIterator
	Implementation for distance-based phylogeny reconstruction iterator. More...
class	DropSpeciesMafIterator
	This iterator removes leaves of a certain species in an attached tree. More...
class	MaximumLikelihoodDistanceEstimationMafIterator
	Compute A simple distance using observed counts. More...
class	MaximumLikelihoodModelFitMafStatistics
	Fit a substitution model. More...
class	NewOutgroupMafIterator
	This iterator root associated trees according to an outgroup sequence. More...
class	OutputTreeMafIterator
	This iterator print an attached tree to a newick file. More...
class	TreeManipulationMafIterator
	This iterator root associated trees according to an outgroup sequence. More...