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