Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::PopGen::Utilities - 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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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]