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]