debian man page for bio::popgen::utilities

Query: bio::popgen::utilities

OS: debian

Section: 3pm

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

Bio::PopGen::Utilities(3pm)				User Contributed Perl Documentation			       Bio::PopGen::Utilities(3pm)

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] perl v5.14.2 2012-03-02 Bio::PopGen::Utilities(3pm)
Related Man Pages
bio::alignio::mega(3pm) - debian
bio::popgen::io(3pm) - debian
bio::popgen::markeri(3pm) - debian
bio::popgen::popstats(3pm) - debian
bio::popgen::utilities(3pm) - debian
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