libsequence
1.9.5
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▼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 |