bpp-popgen/html/SequenceStatistics_8h_source.html

 //

 // File SequenceStatistics.h

 // Authors: Eric Bazin

 //          Sylvain Gaillard

 //          Khalid Belkhir

 //          Benoit Nabholz

 // Created on: Wed Aug 04 2004

 //


 /*

    Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)


    This software is a computer program whose purpose is to provide classes

    for population genetics analysis.


    This software is governed by the CeCILL  license under French law and

    abiding by the rules of distribution of free software.  You can  use,

    modify and/ or redistribute the software under the terms of the CeCILL

    license as circulated by CEA, CNRS and INRIA at the following URL

    "http://www.cecill.info".


    As a counterpart to the access to the source code and  rights to copy,

    modify and redistribute granted by the license, users are provided only

    with a limited warranty  and the software's author,  the holder of the

    economic rights,  and the successive licensors  have only  limited

    liability.


    In this respect, the user's attention is drawn to the risks associated

    with loading,  using,  modifying and/or developing or reproducing the

    software by the user in light of its specific status of free software,

    that may mean  that it is complicated to manipulate,  and  that  also

    therefore means  that it is reserved for developers  and  experienced

    professionals having in-depth computer knowledge. Users are therefore

    encouraged to load and test the software's suitability as regards their

    requirements in conditions enabling the security of their systems and/or

    data to be ensured and,  more generally, to use and operate it in the

    same conditions as regards security.


    The fact that you are presently reading this means that you have had

    knowledge of the CeCILL license and that you accept its terms.

  */


 // 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"


 // From the STL

 #include <string>

 #include <map>

 #include <vector>


 namespace bpp

 {

 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 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

PolymorphismSequenceContainer.h

SiteContainerIterator.h

SiteContainerTools.h

SiteContainer.h

SymbolListTools.h

bpp::GeneticCode

bpp::PolymorphismSequenceContainer
The PolymorphismSequenceContainer class.
Definition: PolymorphismSequenceContainer.h:104

bpp::SequenceStatistics
Static class providing methods to compute statistics on sequences data.
Definition: SequenceStatistics.h:70

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:868

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:586

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:1346

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:1340

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:401

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:1542

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:1454

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:1352

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:611

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:829

bpp::SequenceStatistics::numberOfTriplets
static unsigned int numberOfTriplets(const PolymorphismSequenceContainer &psc, bool gapflag=true)
Compute the number of triplet in an alignment.
Definition: SequenceStatistics.cpp:151

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:648

bpp::SequenceStatistics::numberOfSynonymousSubstitutions
static unsigned int numberOfSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)
compute the number of synonymous subsitutions in an alignment
Definition: SequenceStatistics.cpp:726

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:439

bpp::SequenceStatistics::fstHudson92
static double fstHudson92(const PolymorphismSequenceContainer &psc, size_t id1, size_t id2)
Definition: SequenceStatistics.cpp:954

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:354

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:842

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:312

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:1290

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:1201

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:1395

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:753

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:1653

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:227

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:1362

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:1668

bpp::SequenceStatistics::getNumberOfSingletons_
static unsigned int getNumberOfSingletons_(const Site &site)
Count the number of singleton for a site.
Definition: SequenceStatistics.cpp:1529

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:114

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:710

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:298

bpp::SequenceStatistics::getUsefulValues_
static std::map< std::string, double > getUsefulValues_(size_t n)
Get useful values for theta estimators.
Definition: SequenceStatistics.cpp:1564

bpp::SequenceStatistics::getNumberOfMutations_
static unsigned int getNumberOfMutations_(const Site &site)
Count the number of mutation for a site.
Definition: SequenceStatistics.cpp:1512

bpp::SequenceStatistics::numberOfTransitions
static unsigned int numberOfTransitions(const PolymorphismSequenceContainer &psc)
Return the number of transitions.
Definition: SequenceStatistics.cpp:486

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:92

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:658

bpp::SequenceStatistics::totalNumberOfMutationsOnExternalBranches
static unsigned int totalNumberOfMutationsOnExternalBranches(const PolymorphismSequenceContainer &ing, const PolymorphismSequenceContainer &outg)
Count the total number of mutations in external branchs.
Definition: SequenceStatistics.cpp:188

bpp::SequenceStatistics::generateLdContainer
static PolymorphismSequenceContainer * generateLdContainer(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
generate a special PolymorphismSequenceContainer for linkage disequilbrium analysis
Definition: SequenceStatistics.cpp:997

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:778

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:210

bpp::SequenceStatistics::testUsefulValues
static void testUsefulValues(std::ostream &s, size_t n)
Test useful values.
Definition: SequenceStatistics.cpp:1482

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:134

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:1384

bpp::SequenceStatistics::piSynonymous
static double piSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false)
Compute the synonymous nucleotide diversity, pi.
Definition: SequenceStatistics.cpp:668

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:1334

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:1423

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:257

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:1409

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:171

bpp::SequenceStatistics::numberOfTransversions
static unsigned int numberOfTransversions(const PolymorphismSequenceContainer &psc)
Return the number of transversions.
Definition: SequenceStatistics.cpp:516

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:1123

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:1625

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:816

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:1694

bpp::SequenceStatistics::numberOfNonSynonymousSubstitutions
static unsigned int numberOfNonSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.)
compute the number of non synonymous subsitutions in an alignment
Definition: SequenceStatistics.cpp:740

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:925

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:682

bpp::SequenceStatistics::gcContent
static double gcContent(const PolymorphismSequenceContainer &psc)
Compute the mean GC content in an alignment.
Definition: SequenceStatistics.cpp:249

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:72

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:1437

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:1067

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:1620

bpp::SequenceStatistics::ratioOfTransitionsTransversions
static double ratioOfTransitionsTransversions(const PolymorphismSequenceContainer &psc)
Return the ratio of transitions/transversions.
Definition: SequenceStatistics.cpp:546

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:1234

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:1611

bpp::SequenceStatistics::numberOfSynonymousPolymorphicCodons
static unsigned int numberOfSynonymousPolymorphicCodons(const PolymorphismSequenceContainer &psc, const GeneticCode &gc)
Compute the number of synonymous polymorphic codon sites.
Definition: SequenceStatistics.cpp:634

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:696

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:1373

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:897

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:1328

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:803

bpp::Sequence

bpp::Site

bpp

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