.. _cha_simuPOP_Operators:

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simuPOP Operators
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simuPOP is large, consisting of more than 70 operators and various functions
that covers all important aspects of genetic studies. These includes mutation
(*k*-allele, stepwise, generalized stepwise), migration (arbitrary, can create
new subpopulation), recombination (uniform or nonuniform), gene conversion,
quantitative trait, selection, penetrance (single or multi-locus, hybrid),
ascertainment (case-control, affected sibpairs, random), statistics calculation
(allele, genotype, haplotype, heterozygote number and frequency; expected
heterozygosity; bi-allelic and multi-allelic :math:`D`, :math:`D'` and
:math:`r^{2}` linkage disequilibrium measures; :math:`F_{st}`, :math:`F_{it}`
and :math:`F_{is}`); pedigree tracing, visualization (using R or other Python
modules). This chapter covers the basic and some not-so-basic usages of these
operators, organized roughly by genetic factors.



.. toctree::

   userGuide_ch5_sec1.rst
   userGuide_ch5_sec2.rst
   userGuide_ch5_sec3.rst
   userGuide_ch5_sec4.rst
   userGuide_ch5_sec5.rst
   userGuide_ch5_sec6.rst
   userGuide_ch5_sec7.rst
   userGuide_ch5_sec8.rst
   userGuide_ch5_sec9.rst
   userGuide_ch5_sec10.rst
   userGuide_ch5_sec11.rst
   userGuide_ch5_sec12.rst
   userGuide_ch5_sec13.rst
   userGuide_ch5_sec14.rst