Provided by: libbio-perl-perl_1.7.2-2_all bug


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


         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;


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


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


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AUTHOR - Jason Stajich



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

        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    :

        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)

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