polymorphism

Diversity analyses. More...

Classes
class	BaseDiversity
	Base class of diversity classes. More...
class	BppDiversity
	Computes diversity statistics using third-party library Bio++. More...
class	Consensus::PairwiseConsensus::CharacterContainer
class	Consensus
	Generates consensus sequences. More...
class	FStatistics
	Computes Fis, Fst and Fit from diploid data. More...
class	HaplotypeDiversity
	Computes diversity based on haplotype analysis. More...
class	HFStatistics
	Computes Fst and Fit from haploid data. More...
class	LinkageDisequilibrium
	Analyzes linkage disequilibrium per pair of polymorphic sites. More...
class	MicrosatelliteDiversity
	Analyzes microsatellite data. More...
class	NucleotideDiversity
	Performs analyzes of population genetics. More...
class	SitePolymorphism
	Implements diversity analysis at the site level. More...

Detailed Description

Diversity analyses.

Two classes are contained in this module: NucleotideDiversity, that performs site-centered polymorphism analyses, and HaplotypeDiversity, that performs haplotype-centered analyses. The detection of polymorphic sites is common to both, through the base class BaseDiversity. However this phase must be repeated when stats from the two classes are needed. To reduce the computational burden, the function reserve() can be use, that directly allocates needed memory when the eventual number of polymorphic sites is known prior to analysis (even if not precisely). For both classes, a set of statistics are computed immediately upon load of a data set. For NucleotideDiversity, additional statistics are computed per group upon use of the corresponding accessors. This number of operations performed several times is strictly limited. This is particularly useful when different statistics are needed for a given alignment. However, this system allows not computing unnecessary statistics to a certain extend.