bio::align::proteinstatistics(3pm) [debian man page]

Bio::Align::ProteinStatistics(3pm)			User Contributed Perl Documentation			Bio::Align::ProteinStatistics(3pm)

NAME

       Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)

SYNOPSIS

	 use Bio::Align::ProteinStatistics;
	 use Bio::AlignIO;
	 my $in = Bio::AlignIO->new(-format => 'fasta',
				   -file   => 'pep-104.fasaln');
	 my $aln = $in->next_aln;

	 my $pepstats = Bio::Align::ProteinStatistics->new();
	 $kimura = $protstats->distance(-align => $aln,
					-method => 'Kimura');
	 print $kimura->print_matrix;

DESCRIPTION

       This object is for generating various statistics from a protein alignment.  Mostly it is where pairwise protein distances can be
       calculated.

REFERENCES

       D_Kimura - Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP,
		  Cambridge.

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.org

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Align::ProteinStatistics->new();
	Function: Builds a new Bio::Align::ProteinStatistics object
	Returns : an instance of Bio::Align::ProteinStatistics
	Args	:

   distance
	Title	: distance
	Usage	: my $distance_mat = $stats->distance(-align  => $aln,
						      -method => $method);
	Function: Calculates a distance matrix for all pairwise distances of
		  sequences in an alignment.
	Returns : L<Bio::Matrix::PhylipDist> object
	Args	: -align  => Bio::Align::AlignI object
		  -method => String specifying specific distance method
			     (implementing class may assume a default)

   available_distance_methods
	Title	: available_distance_methods
	Usage	: my @methods = $stats->available_distance_methods();
	Function: Enumerates the possible distance methods
	Returns : Array of strings
	Args	: none

   D - distance methods
   D_Kimura
	Title	: D_Kimura
	Usage	: my $matrix = $pepstats->D_Kimura($aln);
	Function: Calculate Kimura protein distance (Kimura 1983) which
		  approximates PAM distance
		  D = -ln ( 1 - p - 0.2 * p^2 )
	Returns : L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>

   Data Methods
   pairwise_stats
	Title	: pairwise_stats
	Usage	: $obj->pairwise_stats($newval)
	Function:
	Returns : value of pairwise_stats
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02					Bio::Align::ProteinStatistics(3pm)