Class List
Here are the classes, structs, unions and interfaces with brief descriptions:| Sequence::_PolySNPImpl | |
| Sequence::AlignStream< T > | Virtual interface to alignment streams |
| ambiguousNucleotide | |
| Sequence::badFormat | |
| Sequence::chromosome | A chromosome is a container of segments |
| Sequence::ClustalW< T > | ClustalW streams |
| Sequence::Comeron95 | Ka and Ks by Comeron's (1995) method |
| Sequence::ComplementBase | |
| Sequence::countDerivedStates | Functor to count the number of derived states, excluding gaps and missing data, in a range of characters |
| Sequence::countStates | Functor to count the number of states, excluding gaps and missing data, in a range of characters |
| ensureFloating< T, T2, floatingType > | |
| Sequence::Fasta | FASTA sequence stream |
| first_is_equal< key, value > | Functor that checks for equality of first member of two pairs |
| Sequence::FST | Analysis of population structure using  |
| Sequence::Grantham | Grantham's distances |
| Sequence::GranthamWeights2 | Weights paths by Grantham's distances for codons differing at 2 sites |
| Sequence::GranthamWeights3 | Weights paths by Grantham's distances for codons differing at 3 sites |
| Sequence::HKAdata | Data from a single locus for an HKA test |
| Sequence::HKAresults | Results of calculations of the HKA test |
| invalidPolyChar | |
| Sequence::Kimura80 | Kimura's 2-parameter distance |
| Sequence::lowerCrit | Find the upper critical value of a sorted list |
| Sequence::marginal | The genealogy of a portion of a chromosome on which no recombination has occurred |
| Sequence::newick_stream_marginal_tree | Class that provides a typecast-on-output of a marginal tree to a newick tree Example use: |
| Sequence::newick_stream_marginal_tree_impl | |
| Sequence::nmuts< counter > | Calculate the number of mutations at a polymorphic site |
| Sequence::node | A point on a marginal tree at which a coalescent event occurs |
| Sequence::phylipData< T > | |
| Sequence::PolySIM | Analysis of coalescent simulation data |
| Sequence::PolySites | Polymorphism tables for sequence data |
| Sequence::PolySNP | Molecular population genetic analysis |
| Sequence::PolyTable | The base class for polymorphism tables |
| Sequence::PolyTableSlice< T > | A container class for "sliding windows" along a polymorphism table |
| preferFloatingTypes< T, T2 > | |
| Sequence::ProductMoment | Pearson's product-moment correlation |
| Sequence::randomShuffleAdaptor< uni01 > | |
| Sequence::RedundancyCom95 | Calculate redundancy of a genetic code using Comeron's counting scheme |
| Sequence::segment | A portion of a recombining chromosome |
| Sequence::Seq | Abstract interface to sequence objects |
| Sequence::SeqException | Base class for exceptions that may be thrown |
| Sequence::shortestPath | Calculate shortest path between 2 codons |
| Sequence::SimData | Data from coalescent simulations |
| Sequence::SimParams | Parameters for Hudson's simulation program |
| Sequence::SimpleSNP | SNP table data format |
| Sequence::SingleSub | Deal with codons differing at 1 position |
| Sequence::Sites | Calculate length statistics for divergence calculations |
| Sequence::SpearmansRank | Spearman's rank correlation |
| Sequence::ssh | Calculate nucleotide diversity from a polymorphic site |
| Sequence::stateCounter | Keep track of state counts at a site in an alignment or along a sequence |
| Sequence::Sums< T > | |
| Sequence::ThreeSubs | Deal with codons differing at all 3 positions |
| Sequence::TwoSubs | Deal with codons differing at 2 positions |
| Sequence::Unweighted2 | Weights all pathways equally |
| Sequence::Unweighted3 | Weights all pathways equally |
| Sequence::upperCrit | Find the upper critical value of a sorted list |
| Sequence::WeightingScheme2 | Abstract interface to weighting schemes when codons differ at 2 positions |
| Sequence::WeightingScheme3 | Abstract interface to weighting schemes when codons differ at 3 positions |
