libsequence

Introduction

Modules

Divergence Statistics

Classes related to the calculation of Ka and Ks

Classes and functions relating to pathway weighting for Ka/Ks

Classes

Sequence::GranthamWeights2

Sequence::GranthamWeights3

Sequence::Unweighted2

Sequence::Unweighted3

Sequence::WeightingScheme2

Sequence::WeightingScheme3

Classes

Sequence::Comeron95

Sequence::RedundancyCom95

Sequence::SingleSub

Sequence::Sites

Sequence::ThreeSubs

Sequence::TwoSubs

Classes

Sequence::Kimura80

Molecular Population Genetics

Analysis of molecular population genetic data

Namespaces

Sequence::Recombination

Classes

Sequence::FST

Sequence::PolySIM

Sequence::PolySNP

Sequence::PolyTableSlice< T >

Classes Related to Polymorphism tables

Functions

rotatePolyTable

Classes

Sequence::PolySites

Sequence::PolyTable

Sequence::SimData

Sequence::SimpleSNP

Classes and functions related to simulating data under coalescent models

Typedefs

arg

gamete_storage_type

Functions

add_S_inf_sites

add_S_inf_sites

bottleneck

bottleneck

calculate_scales

coalesce

crossover

exponential_change

exponential_change

get_all_descendants

infinite_sites

infinite_sites

infinite_sites

infinite_sites

infinite_sites_sim_data

infinite_sites_sim_data

infinite_sites_sim_data

infinite_sites_sim_data

init_marginal

init_sample

integrate_genetic_map

is_descendant

isseg

neutral_sample

pick2

pick2

pick2_in_deme

pick_branch

pick_spot

pick_spot

pick_uniform_spot

rescale_mutation_positions

sample_length

total_length

total_time

total_time_on_arg

Classes

Sequence::SimData

Sequence::SimParams

Sequence::segment

Sequence::chromosome

Sequence::node

Sequence::marginal

Sequence::newick_stream_marginal_tree

Functions

calcHKA

Classes

Sequence::HKAdata

Sequence::HKAresults

General I/O

Classes for sequence I/O

Classes

Sequence::Fasta

Sequence::Seq

Classes and functions dealing with alignments

Namespaces

Sequence::Alignment

Classes

Sequence::AlignStream< T >

Sequence::ClustalW< T >

Operator overloads

Functions

operator+

operator+

operator+=

operator+=

operator<<

operator<<

operator<<

operator<<

operator<<

operator>>

operator>>

operator>>

operator>>

Statistics

Functions

mean

operator()

variance

Classes

Sequence::ProductMoment

Sequence::SpearmansRank

Sequence::upperCrit

Sequence::lowerCrit

Classes and functions to aid in the calculations of the pathways between two codons

Functions

Intermediates2

Intermediates3

mutsShortestPath

Classes

Sequence::shortestPath

Metaprogramming

Classes

ensureFloating< T, T2, floatingType >

preferFloatingTypes< T, T2 >

Function objects defined in the library

Classes

Sequence::ComplementBase

Sequence::stateCounter

Files

SeqFunctors.hpp

Miscellany

Functions

Translate

Files

Comparisons.hpp

Portability

Classes

Sequence::randomShuffleAdaptor< uni01 >

Class List

Sequence::_PolySNPImpl

Sequence::AlignStream< T >

ambiguousNucleotide

Sequence::badFormat

Sequence::chromosome

Sequence::ClustalW< T >

Sequence::Comeron95

Sequence::ComplementBase

Sequence::countDerivedStates

Sequence::countStates

ensureFloating< T, T2, floatingType >

Sequence::Fasta

first_is_equal< key, value >

Sequence::FST

Sequence::Grantham

Sequence::GranthamWeights2

Sequence::GranthamWeights3

Sequence::gsl_exponential

Sequence::gsl_poisson

Sequence::gsl_uniform

Sequence::gsl_uniform01

Sequence::HKAdata

Sequence::HKAresults

invalidPolyChar

Sequence::Kimura80

Sequence::lowerCrit

Sequence::marginal

Sequence::newick_stream_marginal_tree

Sequence::newick_stream_marginal_tree_impl

Sequence::nmuts< counter >

Sequence::node

Sequence::phylipData< T >

Sequence::PolySIM

Sequence::PolySites

Sequence::PolySNP

Sequence::PolyTable

Sequence::PolyTableSlice< T >

preferFloatingTypes< T, T2 >

Sequence::ProductMoment

Sequence::randomShuffleAdaptor< uni01 >

Sequence::RedundancyCom95

Sequence::segment

Sequence::Seq

Sequence::SeqException

Sequence::sfs_times

Sequence::shortestPath

Sequence::SimData

Sequence::SimParams

Sequence::SimpleSNP

Sequence::SingleSub

Sequence::Sites

Sequence::SpearmansRank

Sequence::ssh

Sequence::stateCounter

Sequence::Sums< T >

Sequence::ThreeSubs

Sequence::TwoSubs

Sequence::uniqueSeq

Sequence::Unweighted2

Sequence::Unweighted3

Sequence::upperCrit

Sequence::WeightingScheme2

Sequence::WeightingScheme3

Class Hierarchy

Sequence::_PolySNPImpl

Sequence::AlignStream< T >

Sequence::ClustalW< T >

Sequence::phylipData< T >

ambiguousNucleotide

Sequence::chromosome

Sequence::Comeron95

Sequence::ComplementBase

Sequence::countDerivedStates

Sequence::countStates

ensureFloating< T, T2, floatingType >

first_is_equal< key, value >

Sequence::FST

Sequence::Grantham

Sequence::gsl_exponential

Sequence::gsl_poisson

Sequence::gsl_uniform

Sequence::gsl_uniform01

Sequence::HKAdata

Sequence::HKAresults

invalidPolyChar

Sequence::Kimura80

Sequence::lowerCrit

Sequence::marginal

Sequence::newick_stream_marginal_tree

Sequence::newick_stream_marginal_tree_impl

Sequence::nmuts< counter >

Sequence::node

Sequence::PolySNP

Sequence::PolySIM

Sequence::PolyTable

Sequence::PolySites

Sequence::SimData

Sequence::SimpleSNP

Sequence::PolyTableSlice< T >

preferFloatingTypes< T, T2 >

Sequence::ProductMoment

Sequence::randomShuffleAdaptor< uni01 >

Sequence::RedundancyCom95

Sequence::segment

Sequence::Seq

Sequence::Fasta

Sequence::SeqException

Sequence::badFormat

Sequence::sfs_times

Sequence::shortestPath

Sequence::SimParams

Sequence::SingleSub

Sequence::Sites

Sequence::SpearmansRank

Sequence::ssh

Sequence::stateCounter

Sequence::Sums< T >

Sequence::ThreeSubs

Sequence::TwoSubs

Sequence::uniqueSeq

Sequence::upperCrit

Sequence::WeightingScheme2

Sequence::GranthamWeights2

Sequence::Unweighted2

Sequence::WeightingScheme3

Sequence::GranthamWeights3

Sequence::Unweighted3

Class Members

Namespace List

Sequence

Sequence::Alignment

Sequence::Recombination

std

Namespace Members

File List

Alignment.hpp

Alignment.tcc

AlignStream.hpp

AlignStream.tcc

Clustalw.hpp

Clustalw.tcc

Coalesce.hpp

Coalesce.tcc

Coalescent.hpp

CoalescentCoalesce.cc

CoalescentFragmentsRescaling.cc

CoalescentInitialize.cc

CoalescentMutation.cc

CoalescentRecombination.cc

CoalescentSimTypes.cc

CoalescentTreeOperations.cc

CodonTable.cc

CodonTable.hpp

Comeron95.cc

Comeron95.hpp

Comparisons.cc

Comparisons.hpp

ComplementBase.cc

ComplementBase.hpp

Correlations.hpp

Correlations.tcc

CountingOperators.hpp

CountingOperators.tcc

Crit.hpp

DemographicModels.hpp

DemographicModels.tcc

descriptiveStats.hpp

descriptiveStats.tcc

ensureFloating.hpp

Fasta.cc

Fasta.hpp

FastaExplicit.hpp

FragmentsRescaling.hpp

FST.cc

FST.hpp

Grantham.cc

Grantham.hpp

GranthamWeights.cc

GranthamWeights.hpp

gsl_rng_wrappers.hpp

HKA.cc

HKA.hpp

Hudson2001.hpp

Initialize.hpp

Kimura80.cc

Kimura80.hpp

Mutation.hpp

Mutation.tcc

NeutralSample.hpp

PathwayHelper.cc

PathwayHelper.hpp

phylipData.hpp

phylipData.tcc

PolyFunctional.hpp

PolySIM.cc

PolySIM.hpp

PolySites.cc

PolySites.hpp

PolySites.tcc

PolySNP.cc

PolySNP.hpp

PolySNPimpl.hpp

PolyTable.cc

PolyTable.hpp

PolyTable.tcc

PolyTableFunctions.cc

PolyTableFunctions.hpp

PolyTableManip.cc

PolyTableManip.hpp

PolyTableSlice.hpp

PolyTableSlice.tcc

preferFloatingTypes.hpp

random_shuffle.hpp

randomShuffleAdaptor.hpp

Recombination.cc

Recombination.hpp

Coalescent/Recombination.hpp

Recombination.tcc

RedundancyCom95.cc

RedundancyCom95.hpp

Seq.cc

Seq.hpp

SeqConstants.cc

SeqConstants.hpp