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)