References to primary sources

General

Stroustrup, B (1997) The C++ Programming Language, 3rd ed. Addison-Wesley. -- The standard language reference
Meyers, S (1998) Effective C++, Second Edition. Addison-Wesley -- An essential reference for design using C++

Sequence::PolySNP

Depaulis, F. and M. Veuille (1998) Mol. Biol. Evol. 1788-1790 -- introduction of number of haplotypes and haplotype diversity as tests of neutrality (Sequence::PolySNP::DandVK, Sequence::PolySNP::DandVH)
Fay, JC, and CI Wu (2000) Genetics 155: 1405-1413 -- definition of Sequence::PolySNP::ThetaH
Fu, YX and WH Li (1993) Genetics 693-709 -- definitions of Fu and Li tests
Hudson, R.R., and N. Kaplan (1985) Genetics 111: 147-164 -- definition of Sequence::Recombination::Minrec
Hudson, R.R. (1987) Genetical Research 50:245-250 -- definition of "Hudson's C" (Sequence::PolySNP::HudsonsC)
Hudson, R.R. et al. (1994) Genetics 136:1329-1340 -- discussion of the "Hudson Haplotype test" (Sequence::PolySIM::HudsonsHaplotypeTest)
Simonsen et al. (1995) Genetics 141: 413 -- power analysis and correction of a Fu and Li test
Tajima, F. (1989) Genetics 123:585-595 -- definition of Tajima's D (Sequence::PolySNP::TajimasD)
Tajima, F. (1993) in Takahata, N. and A.G. Clark (eds) Mechanisms of Molecular Evolution. Sinauer Associates -- general comments on measuring nuceltide diversity (Sequence::PolySNP::ThetaPi), and variances of Pi.
Watterson, G.A. (1975) Theoretical Population Biology 7:256 -- definition of Watterson's Theta (Sequence::PolySNP::ThetaW)

namespace Sequence::Recombination

Hudson, R.R., and N. Kaplan (1985) Genetics 111: 147-164 -- definition of Sequence::Recombination::Minrec
Hudson, R.R. (1987) Genetical Research 50:245-250 -- definition of "Hudson's C" (Sequence::PolySNP::HudsonsC)

Sequence::Comeron95

Comeron, J. (1995) J. Molecular Evolution, 41: 1152-1159.

Sequence::Kimura80

Kimura, M (1980) J. Mol. Evol 16: 111-120.