bpp-popgen/html/SequenceStatistics_8h_source.html

 // SPDX-FileCopyrightText: The Bio++ Development Group

 //

 // SPDX-License-Identifier: CECILL-2.1


 // Secured inclusion of header's file

 #ifndef _SEQUENCESTATISTICS_H_

 #define _SEQUENCESTATISTICS_H_


 // From the bpp-seq library

 #include <Bpp/Seq/SymbolListTools.h>

 #include <Bpp/Seq/Alphabet/CodonAlphabet.h>

 #include <Bpp/Seq/GeneticCode/GeneticCode.h>

 #include <Bpp/Seq/Container/SiteContainerIterator.h>

 #include <Bpp/Seq/Container/SiteContainer.h>

 #include <Bpp/Seq/Container/SiteContainerTools.h>


 #include "PolymorphismSequenceContainer.h"

 #include "PolymorphismSequenceContainerTools.h"


 // From the STL

 #include <string>

 #include <map>

 #include <vector>


 namespace bpp

 {

 using ConstSiteIterator = TemplateSiteIteratorInterface<const Site>;


 class SequenceStatistics

 {

 public:

   static unsigned int numberOfPolymorphicSites(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true);


   static double frequencyOfPolymorphicSites(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true);


   static unsigned int numberOfParsimonyInformativeSites(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static unsigned int numberOfSingletons(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static unsigned int totalNumberOfMutations(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static unsigned int totalNumberOfMutationsOnExternalBranches(

       const PolymorphismSequenceContainer& ing,

       const PolymorphismSequenceContainer& outg);


   static unsigned int numberOfTriplets(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static double heterozygosity(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static double squaredHeterozygosity(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static double gcContent(

       const PolymorphismSequenceContainer& psc);


   static std::vector<unsigned int> gcPolymorphism(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static double watterson75(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true,

       bool scaled = false);


   static double tajima83(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true,

       bool scaled = false);


   static double fayWu2000(

       const PolymorphismSequenceContainer& psc,

       const Sequence& ancestralSites);


   static unsigned int dvk(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static double dvh(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true);


   static unsigned int numberOfTransitions(

       const PolymorphismSequenceContainer& psc);


   static unsigned int numberOfTransversions(

       const PolymorphismSequenceContainer& psc);


   static double ratioOfTransitionsTransversions(

       const PolymorphismSequenceContainer& psc);


   static unsigned int numberOfSitesWithStopCodon(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gCode,

       bool gapflag = true);


   static unsigned int numberOfMonoSitePolymorphicCodons(

       const PolymorphismSequenceContainer& psc,

       bool stopflag = true,

       bool gapflag = true);


   static unsigned int numberOfSynonymousPolymorphicCodons(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc);


   static double watterson75Synonymous(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc);


   static double watterson75NonSynonymous(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc);


   static double piSynonymous(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       bool minchange = false);


   static double piNonSynonymous(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       bool minchange = false);


   static double meanNumberOfSynonymousSites(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       double ratio = 1.);


   static double meanNumberOfNonSynonymousSites(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       double ratio = 1.);


   static unsigned int numberOfSynonymousSubstitutions(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       double freqmin = 0.);


   static unsigned int numberOfNonSynonymousSubstitutions(

       const PolymorphismSequenceContainer& psc,

       const GeneticCode& gc,

       double freqmin = 0.);


   static std::vector<unsigned int> fixedDifferences(

       const PolymorphismSequenceContainer& pscin,

       const PolymorphismSequenceContainer& pscout,

       PolymorphismSequenceContainer& psccons,

       const GeneticCode& gc);


   static std::vector<unsigned int> mkTable(

       const PolymorphismSequenceContainer& ingroup,

       const PolymorphismSequenceContainer& outgroup,

       const GeneticCode& gc,

       double freqmin = 0.);


   static double neutralityIndex(

       const PolymorphismSequenceContainer& ingroup,

       const PolymorphismSequenceContainer& outgroup,

       const GeneticCode& gc,

       double freqmin = 0.);


   static double tajimaDss(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true);


   static double tajimaDtnm(

       const PolymorphismSequenceContainer& psc,

       bool gapflag = true,

       bool ignoreUnknown = true);


   static double fuLiD(

       const PolymorphismSequenceContainer& ingroup,

       const PolymorphismSequenceContainer& outgroup,

       bool useNbSingletons = true,

       bool useNbSegregatingSites = false);


   static double fuLiDStar(

       const PolymorphismSequenceContainer& group,

       bool useNbSegregatingSites = false);


   static double fuLiF(

       const PolymorphismSequenceContainer& ingroup,

       const PolymorphismSequenceContainer& outgroup,

       bool useNbSingletons = true,

       bool useNbSegregatingSites = false);


   static double fuLiFStar(

       const PolymorphismSequenceContainer& group,

       bool useNbSegregatingSites);


   static double fstHudson92(

       const PolymorphismSequenceContainer& psc,

       size_t id1,

       size_t id2);


   static std::unique_ptr<PolymorphismSequenceContainer> generateLdContainer(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble pairwiseDistances1(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble pairwiseDistances2(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble pairwiseD(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble pairwiseDprime(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble pairwiseR2(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double meanD(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double meanDprime(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double meanR2(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double meanDistance1(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double meanDistance2(

       const PolymorphismSequenceContainer& psc,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double originRegressionD(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double originRegressionDprime(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double originRegressionR2(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble linearRegressionD(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble linearRegressionDprime(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static Vdouble linearRegressionR2(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double inverseRegressionR2(

       const PolymorphismSequenceContainer& psc,

       bool distance1 = false,

       bool keepsingleton = true,

       double freqmin = 0.);


   static double hudson87(

       const PolymorphismSequenceContainer& psc,

       double precision = 0.000001,

       double cinf = 0.001,

       double csup = 10000.);


   static void testUsefulValues(

       std::ostream& s,

       size_t n);


 private:

   static unsigned int getNumberOfMutations_(const Site& site);


   static unsigned int getNumberOfSingletons_(const Site& site);


   static unsigned getNumberOfDerivedSingletons_(

       const Site& site_in,

       const Site& site_out);


   static std::map<std::string, double> getUsefulValues_(

       size_t n);


   static double getVD_(

       size_t n,

       double a1,

       double a2,

       double cn);


   static double getUD_(

       double a1,

       double vD);


   static double getVDstar_(

       size_t n,

       double a1,

       double a2,

       double dn);


   static double getUDstar_(

       size_t n,

       double a1,

       double vDs);


   static double leftHandHudson_(

       const PolymorphismSequenceContainer& psc);


   static double rightHandHudson_(

       double c,

       size_t n);


   /************************************************************************/

 };

 } // end of namespace bpp;


 #endif // _SEQUENCESTATISTICS_H_

CodonAlphabet.h

GeneticCode.h

PolymorphismSequenceContainerTools.h

PolymorphismSequenceContainer.h

SiteContainerIterator.h

SiteContainerTools.h

SiteContainer.h

SymbolListTools.h

bpp::GeneticCode

bpp::PolymorphismSequenceContainer
The PolymorphismSequenceContainer class.
Definition: PolymorphismSequenceContainer.h:68

bpp::SequenceStatistics
Static class providing methods to compute statistics on sequences data.
Definition: SequenceStatistics.h:35

bpp::SequenceStatistics::fuLiDStar
static double fuLiDStar(const PolymorphismSequenceContainer &group, bool useNbSegregatingSites=false)
Return the Fu and Li D* test (Fu & Li 1993, Genetics, 133 pp693-709).
Definition: SequenceStatistics.cpp:815

bpp::SequenceStatistics::numberOfSitesWithStopCodon
static unsigned int numberOfSitesWithStopCodon(const PolymorphismSequenceContainer &psc, const GeneticCode &gCode, bool gapflag=true)
Compute the number of codon sites with stop codon.
Definition: SequenceStatistics.cpp:530

bpp::SequenceStatistics::meanDistance1
static double meanDistance1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean pairwise distances between sites / method 1: differences between sequences are not taken in...
Definition: SequenceStatistics.cpp:1314

bpp::SequenceStatistics::meanR2
static double meanR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean R² over all pairwise comparisons
Definition: SequenceStatistics.cpp:1308

bpp::SequenceStatistics::dvk
static unsigned int dvk(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Return the number of haplotype in the sample. Depaulis and Veuille (1998, Mol Biol Evol,...
Definition: SequenceStatistics.cpp:348

bpp::SequenceStatistics::generateLdContainer
static std::unique_ptr< PolymorphismSequenceContainer > generateLdContainer(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
generate a special PolymorphismSequenceContainer for linkage disequilbrium analysis
Definition: SequenceStatistics.cpp:943

bpp::SequenceStatistics::getNumberOfDerivedSingletons_
static unsigned getNumberOfDerivedSingletons_(const Site &site_in, const Site &site_out)
Count the number of singleton for a site.
Definition: SequenceStatistics.cpp:1510

bpp::SequenceStatistics::hudson87
static double hudson87(const PolymorphismSequenceContainer &psc, double precision=0.000001, double cinf=0.001, double csup=10000.)
give estimate of C=4Nr using Hudson method (Hudson 1987, Genet. Res., 50 pp245-250)
Definition: SequenceStatistics.cpp:1422

bpp::SequenceStatistics::meanDistance2
static double meanDistance2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean pairwise distances between sites / method 2: differences between sequences are taken into a...
Definition: SequenceStatistics.cpp:1320

bpp::SequenceStatistics::numberOfMonoSitePolymorphicCodons
static unsigned int numberOfMonoSitePolymorphicCodons(const PolymorphismSequenceContainer &psc, bool stopflag=true, bool gapflag=true)
Compute the number of polymorphic codon with only one mutated site.
Definition: SequenceStatistics.cpp:553

bpp::SequenceStatistics::tajimaDtnm
static double tajimaDtnm(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Return the Tajima's D test (Tajima 1989, Genetics 123 pp 585-595).
Definition: SequenceStatistics.cpp:776

bpp::SequenceStatistics::numberOfTriplets
static unsigned int numberOfTriplets(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Compute the number of triplet in an alignment.
Definition: SequenceStatistics.cpp:112

bpp::SequenceStatistics::watterson75Synonymous
static double watterson75Synonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)
Compute the Watterson(1975,Theor Popul Biol, 7 pp256-276) estimator for synonymous positions.
Definition: SequenceStatistics.cpp:588

bpp::SequenceStatistics::numberOfSynonymousSubstitutions
static unsigned int numberOfSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)
compute the number of synonymous substitutions in an alignment
Definition: SequenceStatistics.cpp:669

bpp::SequenceStatistics::dvh
static double dvh(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Return the haplotype diversity of a sample. Depaulis and Veuille (1998, Mol Biol Evol,...
Definition: SequenceStatistics.cpp:386

bpp::SequenceStatistics::fstHudson92
static double fstHudson92(const PolymorphismSequenceContainer &psc, size_t id1, size_t id2)
Definition: SequenceStatistics.cpp:901

bpp::SequenceStatistics::fayWu2000
static double fayWu2000(const PolymorphismSequenceContainer &psc, const Sequence &ancestralSites)
Compute diversity estimator Theta H (eq. 3) of Fay and Wu (2000, Genetics, 155: 1405-1413)
Definition: SequenceStatistics.cpp:301

bpp::SequenceStatistics::fuLiD
static double fuLiD(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool useNbSingletons=true, bool useNbSegregatingSites=false)
Return the Fu and Li D test (Fu & Li 1993, Genetics, 133 pp693-709).
Definition: SequenceStatistics.cpp:789

bpp::SequenceStatistics::tajima83
static double tajima83(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true, bool scaled=false)
Compute diversity estimator Theta of Tajima (1983, Genetics, 105 pp437-460)
Definition: SequenceStatistics.cpp:260

bpp::SequenceStatistics::pairwiseR2
static Vdouble pairwiseR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of all mean pairwise R² value between two sites (Hill & Robertson 1968,...
Definition: SequenceStatistics.cpp:1255

bpp::SequenceStatistics::pairwiseD
static Vdouble pairwiseD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of all mean pairwise D value between two sites (Lewontin & Kojima 1964,...
Definition: SequenceStatistics.cpp:1160

bpp::SequenceStatistics::linearRegressionD
static Vdouble linearRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope and the origin of the regression |D| = a*distance+b
Definition: SequenceStatistics.cpp:1363

bpp::SequenceStatistics::fixedDifferences
static std::vector< unsigned int > fixedDifferences(const PolymorphismSequenceContainer &pscin, const PolymorphismSequenceContainer &pscout, PolymorphismSequenceContainer &psccons, const GeneticCode &gc)
compute the number of fixed differences between two alignements
Definition: SequenceStatistics.cpp:694

bpp::SequenceStatistics::getUDstar_
static double getUDstar_(size_t n, double a1, double vDs)
Get the uD* value of D* equation in Fu & Li 1993, Genetics, 133 pp693-709)
Definition: SequenceStatistics.cpp:1621

bpp::SequenceStatistics::squaredHeterozygosity
static double squaredHeterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Compute the sum of per site squared heterozygosity in an alignment.
Definition: SequenceStatistics.cpp:183

bpp::SequenceStatistics::originRegressionD
static double originRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope of the regression |D| = 1+a*distance
Definition: SequenceStatistics.cpp:1330

bpp::SequenceStatistics::leftHandHudson_
static double leftHandHudson_(const PolymorphismSequenceContainer &psc)
give the left hand term of equation (4) in Hudson (Hudson 1987, Genet. Res., 50 pp245-250) This term ...
Definition: SequenceStatistics.cpp:1636

bpp::SequenceStatistics::getNumberOfSingletons_
static unsigned int getNumberOfSingletons_(const Site &site)
Count the number of singleton for a site.
Definition: SequenceStatistics.cpp:1497

bpp::SequenceStatistics::numberOfParsimonyInformativeSites
static unsigned int numberOfParsimonyInformativeSites(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Compute the number of parsimony informative sites in an alignment.
Definition: SequenceStatistics.cpp:77

bpp::SequenceStatistics::meanNumberOfNonSynonymousSites
static double meanNumberOfNonSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.)
compute the mean number of non-synonymous site in an alignment
Definition: SequenceStatistics.cpp:655

bpp::SequenceStatistics::watterson75
static double watterson75(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true, bool scaled=false)
Compute diversity estimator Theta of Watterson (1975, Theor Popul Biol, 7 pp256-276)
Definition: SequenceStatistics.cpp:246

bpp::SequenceStatistics::getUsefulValues_
static std::map< std::string, double > getUsefulValues_(size_t n)
Get useful values for theta estimators.
Definition: SequenceStatistics.cpp:1532

bpp::SequenceStatistics::getNumberOfMutations_
static unsigned int getNumberOfMutations_(const Site &site)
Count the number of mutation for a site.
Definition: SequenceStatistics.cpp:1480

bpp::SequenceStatistics::numberOfTransitions
static unsigned int numberOfTransitions(const PolymorphismSequenceContainer &psc)
Return the number of transitions.
Definition: SequenceStatistics.cpp:433

bpp::SequenceStatistics::frequencyOfPolymorphicSites
static double frequencyOfPolymorphicSites(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Compute the frequency of polymorphic site in an alignment.
Definition: SequenceStatistics.cpp:56

bpp::SequenceStatistics::watterson75NonSynonymous
static double watterson75NonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)
Compute the Watterson(1975, Theor Popul Biol, 7 pp256-276) estimator for non synonymous positions.
Definition: SequenceStatistics.cpp:598

bpp::SequenceStatistics::totalNumberOfMutationsOnExternalBranches
static unsigned int totalNumberOfMutationsOnExternalBranches(const PolymorphismSequenceContainer &ing, const PolymorphismSequenceContainer &outg)
Count the total number of mutations in external branches.
Definition: SequenceStatistics.cpp:147

bpp::SequenceStatistics::mkTable
static std::vector< unsigned int > mkTable(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.)
return a vector containing Pa, Ps, Da, Ds
Definition: SequenceStatistics.cpp:720

bpp::SequenceStatistics::heterozygosity
static double heterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Compute the sum of per site heterozygosity in an alignment.
Definition: SequenceStatistics.cpp:167

bpp::SequenceStatistics::testUsefulValues
static void testUsefulValues(std::ostream &s, size_t n)
Test useful values.
Definition: SequenceStatistics.cpp:1450

bpp::SequenceStatistics::numberOfSingletons
static unsigned int numberOfSingletons(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Count the number of singleton nucleotides in an alignment.
Definition: SequenceStatistics.cpp:96

bpp::SequenceStatistics::originRegressionR2
static double originRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope of the regression R² = 1+a*distance
Definition: SequenceStatistics.cpp:1352

bpp::SequenceStatistics::piSynonymous
static double piSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false)
Compute the synonymous nucleotide diversity, pi.
Definition: SequenceStatistics.cpp:610

bpp::SequenceStatistics::meanDprime
static double meanDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean D' over all pairwise comparisons
Definition: SequenceStatistics.cpp:1302

bpp::SequenceStatistics::linearRegressionR2
static Vdouble linearRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope and the origin of the regression R² = a*distance+b
Definition: SequenceStatistics.cpp:1391

bpp::SequenceStatistics::gcPolymorphism
static std::vector< unsigned int > gcPolymorphism(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Return the number of GC alleles and the total number of alleles at polymorphic sites only.
Definition: SequenceStatistics.cpp:212

bpp::SequenceStatistics::linearRegressionDprime
static Vdouble linearRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope and the origin of the regression |D'| = a*distance+b
Definition: SequenceStatistics.cpp:1377

bpp::SequenceStatistics::totalNumberOfMutations
static unsigned int totalNumberOfMutations(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Count the total number of mutations in an alignment.
Definition: SequenceStatistics.cpp:131

bpp::SequenceStatistics::numberOfTransversions
static unsigned int numberOfTransversions(const PolymorphismSequenceContainer &psc)
Return the number of transversions.
Definition: SequenceStatistics.cpp:462

bpp::SequenceStatistics::pairwiseDistances2
static Vdouble pairwiseDistances2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of all mean pairwise distance between two sites to a LD SequencePolymorphismContainer
Definition: SequenceStatistics.cpp:1078

bpp::SequenceStatistics::getVDstar_
static double getVDstar_(size_t n, double a1, double a2, double dn)
Get the vD* value of D* equation in Fu & Li 1993, Genetics, 133 pp693-709)
Definition: SequenceStatistics.cpp:1593

bpp::SequenceStatistics::tajimaDss
static double tajimaDss(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Return the Tajima's D test (Tajima 1989, Genetics 123 pp 585-595).
Definition: SequenceStatistics.cpp:763

bpp::SequenceStatistics::rightHandHudson_
static double rightHandHudson_(double c, size_t n)
give the right hand term of equation (4) in Hudson (Hudson 1987, Genet. Res., 50 pp245-250) This term...
Definition: SequenceStatistics.cpp:1660

bpp::SequenceStatistics::numberOfNonSynonymousSubstitutions
static unsigned int numberOfNonSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)
compute the number of non synonymous substitutions in an alignment
Definition: SequenceStatistics.cpp:682

bpp::SequenceStatistics::fuLiFStar
static double fuLiFStar(const PolymorphismSequenceContainer &group, bool useNbSegregatingSites)
Return the Fu and Li F* test (Fu & Li 1993, Genetics, 133 pp693-709).
Definition: SequenceStatistics.cpp:872

bpp::SequenceStatistics::piNonSynonymous
static double piNonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false)
Compute the non-synonymous nucleotide diversity, pi.
Definition: SequenceStatistics.cpp:625

bpp::SequenceStatistics::gcContent
static double gcContent(const PolymorphismSequenceContainer &psc)
Compute the mean GC content in an alignment.
Definition: SequenceStatistics.cpp:204

bpp::SequenceStatistics::numberOfPolymorphicSites
static unsigned int numberOfPolymorphicSites(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Compute the number of polymorphic site in an alignment.
Definition: SequenceStatistics.cpp:34

bpp::SequenceStatistics::inverseRegressionR2
static double inverseRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope of the regression R² = 1/(1+a*distance)
Definition: SequenceStatistics.cpp:1405

bpp::SequenceStatistics::pairwiseDistances1
static Vdouble pairwiseDistances1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of the pairwise distances between site positions corresponding to a LD SequencePolymo...
Definition: SequenceStatistics.cpp:1015

bpp::SequenceStatistics::getUD_
static double getUD_(double a1, double vD)
Get the uD value of equation (32) in Fu & Li 1993, Genetics, 133 pp693-709)
Definition: SequenceStatistics.cpp:1588

bpp::SequenceStatistics::ratioOfTransitionsTransversions
static double ratioOfTransitionsTransversions(const PolymorphismSequenceContainer &psc)
Return the ratio of transitions/transversions.
Definition: SequenceStatistics.cpp:491

bpp::SequenceStatistics::pairwiseDprime
static Vdouble pairwiseDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of all mean pairwise D' value between two sites (Lewontin 1964, Genetics 49 pp49-67))
Definition: SequenceStatistics.cpp:1196

bpp::SequenceStatistics::getVD_
static double getVD_(size_t n, double a1, double a2, double cn)
Get the vD value of equation (32) in Fu & Li 1993, Genetics, 133 pp693-709)
Definition: SequenceStatistics.cpp:1579

bpp::SequenceStatistics::numberOfSynonymousPolymorphicCodons
static unsigned int numberOfSynonymousPolymorphicCodons(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)
Compute the number of synonymous polymorphic codon sites.
Definition: SequenceStatistics.cpp:575

bpp::SequenceStatistics::meanNumberOfSynonymousSites
static double meanNumberOfSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.)
compute the mean number of synonymous site in an alignment
Definition: SequenceStatistics.cpp:640

bpp::SequenceStatistics::originRegressionDprime
static double originRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.)
give the slope of the regression |D'| = 1+a*distance
Definition: SequenceStatistics.cpp:1341

bpp::SequenceStatistics::fuLiF
static double fuLiF(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool useNbSingletons=true, bool useNbSegregatingSites=false)
Return the Fu and Li F test (Fu & Li 1993, Genetics, 133 pp693-709).
Definition: SequenceStatistics.cpp:844

bpp::SequenceStatistics::meanD
static double meanD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean D over all pairwise comparisons
Definition: SequenceStatistics.cpp:1296

bpp::SequenceStatistics::neutralityIndex
static double neutralityIndex(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.)
return the neutrality index NI = (Pa/Ps)/(Da/Ds) (Rand & Kann 1996, Mol. Biol. Evol....
Definition: SequenceStatistics.cpp:750

bpp::Sequence

bpp::Site

bpp::TemplateSiteIteratorInterface

bpp

bpp::Vdouble
std::vector< double > Vdouble