PopGen

From Biopython
(Difference between revisions)
Jump to: navigation, search
 
(2 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
== Population genetics in Biopython ==
 
== Population genetics in Biopython ==
  
Code pertaining population genetics in Bipython can be found in the PopGen module. Most documentation 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]).
+
Biopython makes available Population Genetics functionality in the Bio.PopGen module.
 +
 
 +
Currently 3 modules are available:
 +
 
 +
#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).
 +
#Coalescent simulation via [http://cmpg.unibe.ch/software/simcoal2/ SimCoal2]
 +
#Selection detection via [http://www.rubic.rdg.ac.uk/~mab/software.html fdist2]
 +
 
 +
 
 +
Documentation on how to access Genepop using Bio.PopGen can be found [[PopGen_Genepop|here]].
 +
 
 +
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]).
  
Currently, most code available wraps existing functionality provided by external programs, namely [http://cmpg.unibe.ch/software/simcoal2/ SimCoal2] for coalescent simulation and [http://www.rubic.rdg.ac.uk/~mab/software.html fdist] for Fst based selection detection.
 
  
 
== Other software ==
 
== Other software ==
  
 
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.
 
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.
 +
 +
[http://www.daimi.au.dk/~mailund/CoaSim/ CoaSim] (coalescent simulation) also exposes a Python interface.
  
 
== Future developments ==
 
== 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.
 +
[[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.

Personal tools
Namespaces
Variants
Actions
Navigation
Toolbox