Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 123]

▼NSequence	The namespace in which this library resides
▼Ncoalsim	Routines for coalescent simulation
Cchromosome	A chromosome is a container of segments
Cmarginal	The genealogy of a portion of a chromosome on which no recombination has occurred
Cnewick_stream_marginal_tree	Class that provides a typecast-on-output of a marginal tree to a newick tree Example use:
Cnewick_stream_marginal_tree_impl
Cnode	A point on a marginal tree at which a coalescent event occurs
Csegment	A portion of a recombining chromosome
▼Ninternal
Ccol_view_	Implementation details for Sequence::ColView and Sequence::ConstColView
Crow_view_	Implementation details for Sequence::RowView and Sequence::ConstRowView
C_PolySNPImpl
CAlignStream	Virtual interface to alignment streams
CAlleleCountMatrix	Matrix representation of allele counts in a VariantMatrix To be constructed
CAlleleCounts
CambiguousNucleotide	Tests if a character is in the set A,G,C,T
CClustalW	ClustalW streams
Ccol_view_iterator	Iterator for column views
CComeron95	Ka and Ks by Comeron's (1995) method
CComplementBase
CcountDerivedStates	Functor to count the number of derived states, excluding gaps and missing data, in a range of characters
CFasta	FASTA sequence stream
Cfastq
CFST	Analysis of population structure using
CGarudStats
CGrantham	Grantham's distances
CGranthamWeights2	Weights paths by Grantham's distances for codons differing at 2 sites
CGranthamWeights3	Weights paths by Grantham's distances for codons differing at 3 sites
CHKAdata	Data from a single locus for an HKA test
CHKAresults	Results of calculations of the HKA test
CinvalidPolyChar	This functor can be used to determine if a range contains characters that the SNP analysis routines in this library cannot handle gracefully
CKimura80	Kimura's 2-parameter distance
Cnmuts	Calculate the number of mutations at a polymorphic site
CnSLiHS
CPairwiseLDstats	Pairwise linkage disequilibrium (LD) stats
CphylipData
CPolySIM	Analysis of coalescent simulation data
CPolySites	Polymorphism tables for sequence data
CPolySNP	Molecular population genetic analysis
CPolyTable	The base class for polymorphism tables
CPolyTableSlice	A container class for "sliding windows" along a polymorphism table
CRedundancyCom95	Calculate redundancy of a genetic code using Comeron's counting scheme
CSeq	Abstract interface to sequence objects
CshortestPath	Calculate shortest path between 2 codons
CSimData	Data from coalescent simulations
CSimParams	Parameters for Hudson's simulation program
CSimpleSNP	SNP table data format
CSingleSub	Deal with codons differing at 1 position
CSites	Calculate length statistics for divergence calculations
CstateCounter	Keep track of state counts at a site in an alignment or along a sequence
CStateCounts	Track character state occurrence at a site in a VariantMatrix
CSums
CThreeSubs	Deal with codons differing at all 3 positions
CTwoSubs	Deal with codons differing at 2 positions
CUnweighted2	Weights all pathways equally
CUnweighted3	Weights all pathways equally
CVariantMatrix	Matrix representation of variation data
CWeightingScheme2	Abstract interface to weighting schemes when codons differ at 2 positions
CWeightingScheme3	Abstract interface to weighting schemes when codons differ at 3 positions
Cfasta_constructors_fixture	\ file FastaConstructors.cc
Cfirst_is_equal	Functor that checks for equality of first member of two pairs
CoutputFreq
Cssh	Calculate nucleotide diversity from a polymorphic site