PopGen modules

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1 Goals of population genetics tools in BioPerl
2 Population genetic modules
3 Some Examples
- 3.1 Read in prettybase data from Seattle SNPs
- 3.2 Run Fu and Li's D
4 References

Goals of population genetics tools in BioPerl

The purpose of these modules is to enable automation of population genomics.

Some papers describe the use of these modules [1] [2] [3] as does the PopGen HOWTO.

Population genetic modules

Bio::PopGen::Statistics - population genetics summary statistics
Bio::PopGen::PopStats - population statistics (Fst)
Bio::PopGen::IO - reading and writing datafiles
Bio::PopGen::Simulation::Coalescent - a very vanilla Coalescent simulator.
Bio::PopGen::Simulation::GeneticDrift - cute genetic drift simulation, does not do recombination

Some Examples

Read in prettybase data from Seattle SNPs

#!/usr/bin/perl -w
use strict;
use Bio::PopGen::IO;
my $in = Bio::PopGen::IO->new(-format => 'prettybase', -file => 'file.prettybase');
my $pop = $in->next_population;
# do something with the population ...

Run Fu and Li's D

#!/usr/bin/perl -w
use strict;
use Bio::PopGen::Statistics;
use Bio::AlignIO;
use Bio::PopGen::Utilities;
 
# pass file on the command line
my $in = Bio::AlignIO->new(-format => 'clustalw', -file => shift @ARGV);
 
# get the 1st alignment from file
if( my $aln = $in->next_aln ) { 
    # get a population object from an alignment
    my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment=>$aln);
 
    my (@ingroup, @outgroup);
    for my $ind ( $pop->get_Individuals) {
	if( $ind->unique_id =~ /^OUT/ ) { 
            # outgroup starts with OUT in this example
	    push @outgroup, $ind;
	} else {
	    push @ingroup, $ind;
	} 
    }
    my $fld = Bio::PopGen::Statistics->fu_and_li_D(\@ingroup,\@outgroup);
    print "$fld\n";
}