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Bio::Align::ProteinStaUseriContributed Perl DoBio::Align::ProteinStatistics(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08  Bio::Align::ProteinStatistics(3)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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