PopGen

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This page will hold documentation for the Bio.PopGen module included with Biopython. For the moment, refer to the PopGen Chapter in the [http://biopython.org/DIST/docs/tutorial/Tutorial.html Tutorial] ([http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]).
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== Population genetics in Biopython ==
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Biopython makes available Population Genetics functionality in the Bio.PopGen module.
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Currently 3 modules are available:
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#Access to Genepop methods (exact tests for Hardy–Weinberg equilibrium, population differentiation, genotypic disequilibrium, F-statistics, null allele frequencies, allele size-based statistics for microsatellites and much more).
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#Coalescent simulation via [http://cmpg.unibe.ch/software/simcoal2/ SimCoal2]
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#Selection detection via [http://www.rubic.rdg.ac.uk/~mab/software.html fdist2]
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Documentation on how to access Genepop using Bio.PopGen can be found [[PopGen_Genepop|here]].
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Documentation for interacting with SimCoal2 and fdist2 can be found on the PopGen Chapter in the [http://biopython.org/DIST/docs/tutorial/Tutorial.html Tutorial] ([http://biopython.org/DIST/docs/tutorial/Tutorial.pdf PDF]).
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== Other software ==
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Python programmers might want to consider [http://pypop.org PyPop] which includes intra-population frequentist statistics and [http://simupop.sourceforge.net/ simuPOP] for foward-time population genetics.
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[http://www.daimi.au.dk/~mailund/CoaSim/ CoaSim] (coalescent simulation) also exposes a Python interface.
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== Future developments ==
  
 
Any notes (or discussion) about possible future developments should be restricted to the [[PopGen_dev|PopGen development]] page.
 
Any notes (or discussion) about possible future developments should be restricted to the [[PopGen_dev|PopGen development]] page.
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[[Category:Wiki Documentation]]

Latest revision as of 12:11, 17 November 2009

Population genetics in Biopython

Biopython makes available Population Genetics functionality in the Bio.PopGen module.

Currently 3 modules are available:

  1. Access to Genepop methods (exact tests for Hardy–Weinberg equilibrium, population differentiation, genotypic disequilibrium, F-statistics, null allele frequencies, allele size-based statistics for microsatellites and much more).
  2. Coalescent simulation via SimCoal2
  3. Selection detection via fdist2


Documentation on how to access Genepop using Bio.PopGen can be found here.

Documentation for interacting with SimCoal2 and fdist2 can be found on the PopGen Chapter in the Tutorial (PDF).


Other software

Python programmers might want to consider PyPop which includes intra-population frequentist statistics and simuPOP for foward-time population genetics.

CoaSim (coalescent simulation) also exposes a Python interface.

Future developments

Any notes (or discussion) about possible future developments should be restricted to the PopGen development page.

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