libsequence  1.9.5
Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 12]
 CSequence::_PolySNPImpl
 CSequence::AlignStream< T >Virtual interface to alignment streams
 CSequence::ClustalW< T >ClustalW streams
 CSequence::phylipData< T >
 CSequence::AlleleCountMatrixMatrix representation of allele counts in a VariantMatrix To be constructed
 CSequence::AlleleCounts
 CSequence::ambiguousNucleotideTests if a character is in the set A,G,C,T
 CSequence::coalsim::chromosomeA chromosome is a container of segments
 CSequence::internal::col_view_< T >Implementation details for Sequence::ColView and Sequence::ConstColView
 CSequence::col_view_iterator< POINTER >Iterator for column views
 CSequence::Comeron95Ka and Ks by Comeron's (1995) method
 CSequence::ComplementBase
 CSequence::countDerivedStatesFunctor to count the number of derived states, excluding gaps and missing data, in a range of characters
 Cfasta_constructors_fixture\ file FastaConstructors.cc
 Cfirst_is_equal< key, value >Functor that checks for equality of first member of two pairs
 CSequence::FSTAnalysis of population structure using $F_{ST}$
 CSequence::GarudStats
 CSequence::GranthamGrantham's distances
 CSequence::HKAdataData from a single locus for an HKA test
 CSequence::HKAresultsResults of calculations of the HKA test
 CSequence::invalidPolyCharThis functor can be used to determine if a range contains characters that the SNP analysis routines in this library cannot handle gracefully
 CSequence::Kimura80Kimura's 2-parameter distance
 CSequence::coalsim::marginalThe genealogy of a portion of a chromosome on which no recombination has occurred
 CSequence::coalsim::newick_stream_marginal_treeClass that provides a typecast-on-output of a marginal tree to a newick tree Example use:
 CSequence::coalsim::newick_stream_marginal_tree_impl
 CSequence::nmuts< counter >Calculate the number of mutations at a polymorphic site
 CSequence::coalsim::nodeA point on a marginal tree at which a coalescent event occurs
 CSequence::nSLiHS
 CoutputFreq
 CSequence::PairwiseLDstatsPairwise linkage disequilibrium (LD) stats

 
 CSequence::PolySIMAnalysis of coalescent simulation data
 CSequence::PolySNPMolecular population genetic analysis
 CSequence::PolyTableThe base class for polymorphism tables
 CSequence::PolySitesPolymorphism tables for sequence data
 CSequence::PolyTableSlice< T >A container class for "sliding windows" along a polymorphism table
 CSequence::RedundancyCom95Calculate redundancy of a genetic code using Comeron's counting scheme
 CSequence::internal::row_view_< T >Implementation details for Sequence::RowView and Sequence::ConstRowView
 CSequence::coalsim::segmentA portion of a recombining chromosome
 CSequence::SeqAbstract interface to sequence objects
 CSequence::FastaFASTA sequence stream
 CSequence::fastq
 CSequence::shortestPathCalculate shortest path between 2 codons
 CSequence::SimDataData from coalescent simulations
 CSequence::SimParamsParameters for Hudson's simulation program
 CSequence::SimpleSNPSNP table data format
 CSequence::SingleSubDeal with codons differing at 1 position
 CSequence::SitesCalculate length statistics for divergence calculations
 CsshCalculate nucleotide diversity from a polymorphic site
 CSequence::stateCounterKeep track of state counts at a site in an alignment or along a sequence
 CSequence::StateCountsTrack character state occurrence at a site in a VariantMatrix
 CSequence::Sums< T >
 CSequence::ThreeSubsDeal with codons differing at all 3 positions
 CSequence::TwoSubsDeal with codons differing at 2 positions
 CSequence::VariantMatrixMatrix representation of variation data
 CSequence::WeightingScheme2Abstract interface to weighting schemes when codons differ at 2 positions
 CSequence::GranthamWeights2Weights paths by Grantham's distances for codons differing at 2 sites
 CSequence::Unweighted2Weights all pathways equally
 CSequence::WeightingScheme3Abstract interface to weighting schemes when codons differ at 3 positions
 CSequence::GranthamWeights3Weights paths by Grantham's distances for codons differing at 3 sites
 CSequence::Unweighted3Weights all pathways equally