biopython

v1.71.0

biopython v1.71.0 Bio.PopGen.GenePop.EasyController.EasyController

Initializes the controller.

genepop_dir is the directory where GenePop is.

The binary should be called Genepop (capital G)

Link to this section Summary

Functions

__init__()
estimate_nm()

Estimate Nm. Just a simple bridge

get_alleles()

Returns the alleles for a certain population and locus

get_alleles_all_pops()

Returns the alleles for a certain population and locus

get_f_stats()

Returns F stats for a locus

get_fis()

Returns the Fis for a certain population and locus

get_genotype_count()

Returns the genotype counts for a certain population and locus

get_heterozygosity_info()

Returns the heterozygosity info for a certain locus on a population

get_multilocus_f_stats()

Returns the multilocus F stats

Link to this section Functions

Link to this function __init__()
Link to this function estimate_nm()

Estimate Nm. Just a simple bridge.

Link to this function get_alleles()

Returns the alleles for a certain population and locus.

Link to this function get_alleles_all_pops()

Returns the alleles for a certain population and locus.

Link to this function get_f_stats()

Returns F stats for a locus.

Returns Fis(CW), Fst, Fit, Qintra, Qinter

Link to this function get_fis()

Returns the Fis for a certain population and locus.

Below CW means Cockerham and Weir and RH means Robertson and Hill.

Returns a pair:

  • dictionary [allele] = (repetition count, frequency, Fis CW ) with information for each allele
  • a triple with total number of alleles, Fis CW, Fis RH
Link to this function get_genotype_count()

Returns the genotype counts for a certain population and locus.

Link to this function get_heterozygosity_info()

Returns the heterozygosity info for a certain locus on a population.

Returns (Expected homozygotes, observed homozygotes, Expected heterozygotes, observed heterozygotes)

Link to this function get_multilocus_f_stats()

Returns the multilocus F stats.

Explain averaging. Returns Fis(CW), Fst, Fit