bpp-core3  3.0.0
SequenceStatistics.h
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1 // SPDX-FileCopyrightText: The Bio++ Development Group
2 //
3 // SPDX-License-Identifier: CECILL-2.1
4 
5 // Secured inclusion of header's file
6 #ifndef _SEQUENCESTATISTICS_H_
7 #define _SEQUENCESTATISTICS_H_
8 
9 // From the bpp-seq library
10 #include <Bpp/Seq/SymbolListTools.h>
11 #include <Bpp/Seq/Alphabet/CodonAlphabet.h>
12 #include <Bpp/Seq/GeneticCode/GeneticCode.h>
13 #include <Bpp/Seq/Container/SiteContainerIterator.h>
14 #include <Bpp/Seq/Container/SiteContainer.h>
15 #include <Bpp/Seq/Container/SiteContainerTools.h>
16 
17 #include "PolymorphismSequenceContainer.h"
18 #include "PolymorphismSequenceContainerTools.h"
19 
20 // From the STL
21 #include <string>
22 #include <map>
23 #include <vector>
24 
25 namespace bpp
26 {
27 using ConstSiteIterator = TemplateSiteIteratorInterface<const Site>;
28 
34 class SequenceStatistics
35 {
36 public:
52  static unsigned int numberOfPolymorphicSites(
53  const PolymorphismSequenceContainer& psc,
54  bool gapflag = true,
55  bool ignoreUnknown = true);
56 
73  static double frequencyOfPolymorphicSites(
74  const PolymorphismSequenceContainer& psc,
75  bool gapflag = true,
76  bool ignoreUnknown = true);
77 
85  static unsigned int numberOfParsimonyInformativeSites(
86  const PolymorphismSequenceContainer& psc,
87  bool gapflag = true);
88 
97  static unsigned int numberOfSingletons(
98  const PolymorphismSequenceContainer& psc,
99  bool gapflag = true);
100 
111  static unsigned int totalNumberOfMutations(
112  const PolymorphismSequenceContainer& psc,
113  bool gapflag = true);
114 
127  static unsigned int totalNumberOfMutationsOnExternalBranches(
128  const PolymorphismSequenceContainer& ing,
129  const PolymorphismSequenceContainer& outg);
130 
138  static unsigned int numberOfTriplets(
139  const PolymorphismSequenceContainer& psc,
140  bool gapflag = true);
141 
148  static double heterozygosity(
149  const PolymorphismSequenceContainer& psc,
150  bool gapflag = true);
151 
159  static double squaredHeterozygosity(
160  const PolymorphismSequenceContainer& psc,
161  bool gapflag = true);
162 
168  static double gcContent(
169  const PolymorphismSequenceContainer& psc);
170 
185  static std::vector<unsigned int> gcPolymorphism(
186  const PolymorphismSequenceContainer& psc,
187  bool gapflag = true);
188 
207  static double watterson75(
208  const PolymorphismSequenceContainer& psc,
209  bool gapflag = true,
210  bool ignoreUnknown = true,
211  bool scaled = false);
212 
234  static double tajima83(
235  const PolymorphismSequenceContainer& psc,
236  bool gapflag = true,
237  bool ignoreUnknown = true,
238  bool scaled = false);
239 
248  static double fayWu2000(
249  const PolymorphismSequenceContainer& psc,
250  const Sequence& ancestralSites);
251 
264  static unsigned int dvk(
265  const PolymorphismSequenceContainer& psc,
266  bool gapflag = true);
267 
280  static double dvh(
281  const PolymorphismSequenceContainer& psc,
282  bool gapflag = true);
283 
290  static unsigned int numberOfTransitions(
291  const PolymorphismSequenceContainer& psc);
292 
299  static unsigned int numberOfTransversions(
300  const PolymorphismSequenceContainer& psc);
301 
308  static double ratioOfTransitionsTransversions(
309  const PolymorphismSequenceContainer& psc);
310 
320  static unsigned int numberOfSitesWithStopCodon(
321  const PolymorphismSequenceContainer& psc,
322  const GeneticCode& gCode,
323  bool gapflag = true);
324 
337  static unsigned int numberOfMonoSitePolymorphicCodons(
338  const PolymorphismSequenceContainer& psc,
339  bool stopflag = true,
340  bool gapflag = true);
341 
352  static unsigned int numberOfSynonymousPolymorphicCodons(
353  const PolymorphismSequenceContainer& psc,
354  const GeneticCode& gc);
355 
370  static double watterson75Synonymous(
371  const PolymorphismSequenceContainer& psc,
372  const GeneticCode& gc);
373 
388  static double watterson75NonSynonymous(
389  const PolymorphismSequenceContainer& psc,
390  const GeneticCode& gc);
391 
407  static double piSynonymous(
408  const PolymorphismSequenceContainer& psc,
409  const GeneticCode& gc,
410  bool minchange = false);
411 
427  static double piNonSynonymous(
428  const PolymorphismSequenceContainer& psc,
429  const GeneticCode& gc,
430  bool minchange = false);
431 
446  static double meanNumberOfSynonymousSites(
447  const PolymorphismSequenceContainer& psc,
448  const GeneticCode& gc,
449  double ratio = 1.);
450 
464  static double meanNumberOfNonSynonymousSites(
465  const PolymorphismSequenceContainer& psc,
466  const GeneticCode& gc,
467  double ratio = 1.);
468 
484  static unsigned int numberOfSynonymousSubstitutions(
485  const PolymorphismSequenceContainer& psc,
486  const GeneticCode& gc,
487  double freqmin = 0.);
488 
504  static unsigned int numberOfNonSynonymousSubstitutions(
505  const PolymorphismSequenceContainer& psc,
506  const GeneticCode& gc,
507  double freqmin = 0.);
508 
526  static std::vector<unsigned int> fixedDifferences(
527  const PolymorphismSequenceContainer& pscin,
528  const PolymorphismSequenceContainer& pscout,
529  PolymorphismSequenceContainer& psccons,
530  const GeneticCode& gc);
531 
543  static std::vector<unsigned int> mkTable(
544  const PolymorphismSequenceContainer& ingroup,
545  const PolymorphismSequenceContainer& outgroup,
546  const GeneticCode& gc,
547  double freqmin = 0.);
548 
562  static double neutralityIndex(
563  const PolymorphismSequenceContainer& ingroup,
564  const PolymorphismSequenceContainer& outgroup,
565  const GeneticCode& gc,
566  double freqmin = 0.);
567 
585  static double tajimaDss(
586  const PolymorphismSequenceContainer& psc,
587  bool gapflag = true,
588  bool ignoreUnknown = true);
589 
605  static double tajimaDtnm(
606  const PolymorphismSequenceContainer& psc,
607  bool gapflag = true,
608  bool ignoreUnknown = true);
609 
628  static double fuLiD(
629  const PolymorphismSequenceContainer& ingroup,
630  const PolymorphismSequenceContainer& outgroup,
631  bool useNbSingletons = true,
632  bool useNbSegregatingSites = false);
633 
643  static double fuLiDStar(
644  const PolymorphismSequenceContainer& group,
645  bool useNbSegregatingSites = false);
646 
665  static double fuLiF(
666  const PolymorphismSequenceContainer& ingroup,
667  const PolymorphismSequenceContainer& outgroup,
668  bool useNbSingletons = true,
669  bool useNbSegregatingSites = false);
670 
680  static double fuLiFStar(
681  const PolymorphismSequenceContainer& group,
682  bool useNbSegregatingSites);
683 
702  static double fstHudson92(
703  const PolymorphismSequenceContainer& psc,
704  size_t id1,
705  size_t id2);
706 
707 
734  static std::unique_ptr<PolymorphismSequenceContainer> generateLdContainer(
735  const PolymorphismSequenceContainer& psc,
736  bool keepsingleton = true,
737  double freqmin = 0.);
738 
752  static Vdouble pairwiseDistances1(
753  const PolymorphismSequenceContainer& psc,
754  bool keepsingleton = true,
755  double freqmin = 0.);
756 
771  static Vdouble pairwiseDistances2(
772  const PolymorphismSequenceContainer& psc,
773  bool keepsingleton = true,
774  double freqmin = 0.);
775 
788  static Vdouble pairwiseD(
789  const PolymorphismSequenceContainer& psc,
790  bool keepsingleton = true,
791  double freqmin = 0.);
792 
805  static Vdouble pairwiseDprime(
806  const PolymorphismSequenceContainer& psc,
807  bool keepsingleton = true,
808  double freqmin = 0.);
809 
822  static Vdouble pairwiseR2(
823  const PolymorphismSequenceContainer& psc,
824  bool keepsingleton = true,
825  double freqmin = 0.);
826 
839  static double meanD(
840  const PolymorphismSequenceContainer& psc,
841  bool keepsingleton = true,
842  double freqmin = 0.);
843 
856  static double meanDprime(
857  const PolymorphismSequenceContainer& psc,
858  bool keepsingleton = true,
859  double freqmin = 0.);
860 
873  static double meanR2(
874  const PolymorphismSequenceContainer& psc,
875  bool keepsingleton = true,
876  double freqmin = 0.);
877 
889  static double meanDistance1(
890  const PolymorphismSequenceContainer& psc,
891  bool keepsingleton = true,
892  double freqmin = 0.);
893 
905  static double meanDistance2(
906  const PolymorphismSequenceContainer& psc,
907  bool keepsingleton = true,
908  double freqmin = 0.);
909 
926  static double originRegressionD(
927  const PolymorphismSequenceContainer& psc,
928  bool distance1 = false,
929  bool keepsingleton = true,
930  double freqmin = 0.);
931 
948  static double originRegressionDprime(
949  const PolymorphismSequenceContainer& psc,
950  bool distance1 = false,
951  bool keepsingleton = true,
952  double freqmin = 0.);
953 
970  static double originRegressionR2(
971  const PolymorphismSequenceContainer& psc,
972  bool distance1 = false,
973  bool keepsingleton = true,
974  double freqmin = 0.);
975 
992  static Vdouble linearRegressionD(
993  const PolymorphismSequenceContainer& psc,
994  bool distance1 = false,
995  bool keepsingleton = true,
996  double freqmin = 0.);
997 
1014  static Vdouble linearRegressionDprime(
1015  const PolymorphismSequenceContainer& psc,
1016  bool distance1 = false,
1017  bool keepsingleton = true,
1018  double freqmin = 0.);
1019 
1036  static Vdouble linearRegressionR2(
1037  const PolymorphismSequenceContainer& psc,
1038  bool distance1 = false,
1039  bool keepsingleton = true,
1040  double freqmin = 0.);
1041 
1059  static double inverseRegressionR2(
1060  const PolymorphismSequenceContainer& psc,
1061  bool distance1 = false,
1062  bool keepsingleton = true,
1063  double freqmin = 0.);
1064 
1074  static double hudson87(
1075  const PolymorphismSequenceContainer& psc,
1076  double precision = 0.000001,
1077  double cinf = 0.001,
1078  double csup = 10000.);
1079 
1086  static void testUsefulValues(
1087  std::ostream& s,
1088  size_t n);
1089 
1090 private:
1094  static unsigned int getNumberOfMutations_(const Site& site);
1095 
1099  static unsigned int getNumberOfSingletons_(const Site& site);
1100 
1108  static unsigned getNumberOfDerivedSingletons_(
1109  const Site& site_in,
1110  const Site& site_out);
1111 
1145  static std::map<std::string, double> getUsefulValues_(
1146  size_t n);
1147 
1160  static double getVD_(
1161  size_t n,
1162  double a1,
1163  double a2,
1164  double cn);
1165 
1176  static double getUD_(
1177  double a1,
1178  double vD);
1179 
1192  static double getVDstar_(
1193  size_t n,
1194  double a1,
1195  double a2,
1196  double dn);
1197 
1209  static double getUDstar_(
1210  size_t n,
1211  double a1,
1212  double vDs);
1213 
1219  static double leftHandHudson_(
1220  const PolymorphismSequenceContainer& psc);
1221 
1226  static double rightHandHudson_(
1227  double c,
1228  size_t n);
1229 
1230  /************************************************************************/
1231 };
1232 } // end of namespace bpp;
1233 
1234 #endif // _SEQUENCESTATISTICS_H_
bpp::SequenceStatistics::getNumberOfSingletons_
static unsigned int getNumberOfSingletons_(const Site &site)
Count the number of singleton for a site.
Definition: SequenceStatistics.cpp:1497
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::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::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::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::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::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::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. 13 pp735-748)
Definition: SequenceStatistics.cpp:750
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&#39;| = 1+a*distance
Definition: SequenceStatistics.cpp:1341
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::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
Definition: AlleleInfo.h:13
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::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::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::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::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::tajimaDtnm
static double tajimaDtnm(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Return the Tajima&#39;s D test (Tajima 1989, Genetics 123 pp 585-595).
Definition: SequenceStatistics.cpp:776
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::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::testUsefulValues
static void testUsefulValues(std::ostream &s, size_t n)
Test useful values.
Definition: SequenceStatistics.cpp:1450
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::ConstSiteIterator
TemplateSiteIteratorInterface< const Site > ConstSiteIterator
Definition: SequenceStatistics.h:27
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::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::gcContent
static double gcContent(const PolymorphismSequenceContainer &psc)
Compute the mean GC content in an alignment.
Definition: SequenceStatistics.cpp:204
bpp::SequenceStatistics::meanDprime
static double meanDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give mean D&#39; over all pairwise comparisons
Definition: SequenceStatistics.cpp:1302
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::ratioOfTransitionsTransversions
static double ratioOfTransitionsTransversions(const PolymorphismSequenceContainer &psc)
Return the ratio of transitions/transversions.
Definition: SequenceStatistics.cpp:491
bpp::SequenceStatistics::fstHudson92
static double fstHudson92(const PolymorphismSequenceContainer &psc, size_t id1, size_t id2)
Definition: SequenceStatistics.cpp:901
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::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&#39;| = a*distance+b
Definition: SequenceStatistics.cpp:1377
bpp::SequenceStatistics::tajimaDss
static double tajimaDss(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true)
Return the Tajima&#39;s D test (Tajima 1989, Genetics 123 pp 585-595).
Definition: SequenceStatistics.cpp:763
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::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::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::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::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::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
Static class providing methods to compute statistics on sequences data.
Definition: SequenceStatistics.h:34
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::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::numberOfTransversions
static unsigned int numberOfTransversions(const PolymorphismSequenceContainer &psc)
Return the number of transversions.
Definition: SequenceStatistics.cpp:462
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::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::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::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::numberOfTransitions
static unsigned int numberOfTransitions(const PolymorphismSequenceContainer &psc)
Return the number of transitions.
Definition: SequenceStatistics.cpp:433
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, 12 pp1788-1790)
Definition: SequenceStatistics.cpp:386
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::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::pairwiseDprime
static Vdouble pairwiseDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.)
give the vector of all mean pairwise D&#39; value between two sites (Lewontin 1964, Genetics 49 pp49-67))...
Definition: SequenceStatistics.cpp:1196
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::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::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::PolymorphismSequenceContainer
The PolymorphismSequenceContainer class.
Definition: PolymorphismSequenceContainer.h:66
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::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::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::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::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::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::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::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::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::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::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::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::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::getNumberOfMutations_
static unsigned int getNumberOfMutations_(const Site &site)
Count the number of mutation for a site.
Definition: SequenceStatistics.cpp:1480
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::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::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