NAME

       Bio::PopGen::Utilities - Utilities for working with PopGen data and objects

SYNOPSIS

         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);

DESCRIPTION

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

   aln_to_population
        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]