| Bio::Align::ProteinStatistics(3pm) | User Contributed Perl Documentation | Bio::Align::ProteinStatistics(3pm) |
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.
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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)
| 2018-10-27 | perl v5.26.2 |