Bio::PopGen::Utilities(3) Utilities for working with PopGen data and objects


use Bio::PopGen::Utilities;
use Bio::AlignIO;
my $in = Bio::AlignIO->new(-file => 't/data/t7.aln',
-format => 'clustalw');
my $aln = $in->next_aln;
# get a population, each sequence is an individual and
# for the default case, every site which is not monomorphic
# is a 'marker'. Each individual will have a 'genotype' for the
# site which will be the specific base in the alignment at that
# site
my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment => $aln);
# get the synonymous sites from the alignemt only as the 'genotypes'
# for the population
my $synpop = Bio::PopGen::Utilities->aln_to_population(-site_model => 'cod',
-alignment => $aln);


This object provides some convience function to turn sequence alignments into usable objects for the Population genetics modules (Bio::PopGen).


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Reporting Bugs

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AUTHOR - Jason Stajich

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : aln_to_population
 Usage   : my $pop = Bio::PopGen::Utilities->aln_to_population($aln);
 Function: Turn and alignment into a set of L<Bio::PopGen::Individual>
           objects grouped in a L<Bio::PopGen::Population> object
           Sites are treated as 'Markers' in the Bioperl PopGen object
           model in the sense that a site is a unique location for which
           an individual will have a genotype (a set of alleles). 
           In this implementation we are assuming that each individual 
           has a single entry in the alignment file.
           Specify a site model as one of those listed
           'all' -- every base in the alignment is considered a site
           'cod' -- codons 
           The option -site_model
                for All sites          : 'all' 
                    Codon sites        : 'cod' or 'codon'
          To see all sites, including those which are fixed in the population
          add -include_monomorphic => 1
          to the arguments
 Returns : 
 Args    : -include_monomorphic => 1   to specify all sites, 
                                       even those which are monomorphic
                                       in the population 
                                  (useful for HKA test mostly) 
                            [default is false]
           -phase          => specify a phase for the data, this is only
                              used if the site_mode is codon
                            [default is 0]
           -site_model     => one-of 'all', 'codon'
                             to specify a site model for the data extraction
                             from the alignment
                            [default is all]
           -alignment      => provide a L<Bio::SimpleAlign> object [required]