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

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, Cambridge.

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

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.

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

Email jason-at-bioperl.org

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

 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>

 Title   : pairwise_stats
 Usage   : $obj->pairwise_stats($newval)
 Function: 
 Returns : value of pairwise_stats
 Args    : newvalue (optional)
2019-12-07 perl v5.32.1

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