libsequence  1.9.5
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
 NSequenceThe namespace in which this library resides
 NcoalsimRoutines for coalescent simulation
 CchromosomeA chromosome is a container of segments
 CmarginalThe genealogy of a portion of a chromosome on which no recombination has occurred
 Cnewick_stream_marginal_treeClass that provides a typecast-on-output of a marginal tree to a newick tree Example use:
 Cnewick_stream_marginal_tree_impl
 CnodeA point on a marginal tree at which a coalescent event occurs
 CsegmentA 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
 CAlignStreamVirtual interface to alignment streams
 CAlleleCountMatrixMatrix representation of allele counts in a VariantMatrix To be constructed
 CAlleleCounts
 CambiguousNucleotideTests if a character is in the set A,G,C,T
 CClustalWClustalW streams
 Ccol_view_iteratorIterator for column views
 CComeron95Ka and Ks by Comeron's (1995) method
 CComplementBase
 CcountDerivedStatesFunctor to count the number of derived states, excluding gaps and missing data, in a range of characters
 CFastaFASTA sequence stream
 Cfastq
 CFSTAnalysis of population structure using $F_{ST}$
 CGarudStats
 CGranthamGrantham's distances
 CGranthamWeights2Weights paths by Grantham's distances for codons differing at 2 sites
 CGranthamWeights3Weights paths by Grantham's distances for codons differing at 3 sites
 CHKAdataData from a single locus for an HKA test
 CHKAresultsResults of calculations of the HKA test
 CinvalidPolyCharThis functor can be used to determine if a range contains characters that the SNP analysis routines in this library cannot handle gracefully
 CKimura80Kimura's 2-parameter distance
 CnmutsCalculate the number of mutations at a polymorphic site
 CnSLiHS
 CPairwiseLDstatsPairwise linkage disequilibrium (LD) stats

 
 CphylipData
 CPolySIMAnalysis of coalescent simulation data
 CPolySitesPolymorphism tables for sequence data
 CPolySNPMolecular population genetic analysis
 CPolyTableThe base class for polymorphism tables
 CPolyTableSliceA container class for "sliding windows" along a polymorphism table
 CRedundancyCom95Calculate redundancy of a genetic code using Comeron's counting scheme
 CSeqAbstract interface to sequence objects
 CshortestPathCalculate shortest path between 2 codons
 CSimDataData from coalescent simulations
 CSimParamsParameters for Hudson's simulation program
 CSimpleSNPSNP table data format
 CSingleSubDeal with codons differing at 1 position
 CSitesCalculate length statistics for divergence calculations
 CstateCounterKeep track of state counts at a site in an alignment or along a sequence
 CStateCountsTrack character state occurrence at a site in a VariantMatrix
 CSums
 CThreeSubsDeal with codons differing at all 3 positions
 CTwoSubsDeal with codons differing at 2 positions
 CUnweighted2Weights all pathways equally
 CUnweighted3Weights all pathways equally
 CVariantMatrixMatrix representation of variation data
 CWeightingScheme2Abstract interface to weighting schemes when codons differ at 2 positions
 CWeightingScheme3Abstract interface to weighting schemes when codons differ at 3 positions
 Cfasta_constructors_fixture\ file FastaConstructors.cc
 Cfirst_is_equalFunctor that checks for equality of first member of two pairs
 CoutputFreq
 CsshCalculate nucleotide diversity from a polymorphic site