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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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]