Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
use Bio::Align::DNAStatistics;
use Bio::AlignIO;
my $stats = new Bio::Align::PairwiseStatistics;
my $alignin = new Bio::AlignIO(-format => 'emboss',
-file => 't/data/insulin.water');
my $jc = $stats->distance($aln, 'Jukes-Cantor');
foreach my $r ( @$jc ) {
print "\t";
foreach my $r ( @$d ) {
print "$r\t";
}
print "\n";
}
This object contains routines for calculating various statistics and distances for DNA alignments. The routines are not well tested and do contain errors at this point. Work is underway to correct them, but do not expect this code to give you the right answer currently! Use dnadist/distmat in the PHLYIP or EMBOSS packages to calculate the distances.
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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 = new Bio::Align::DNAStatistics(); Function: Builds a new Bio::Align::DNAStatistics object Returns : Bio::Align::DNAStatistics Args : none
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 : Array ref
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_JukesCantor
Usage : my $d = $stat->D_JukesCantor($aln)
Function: Calculates D (pairwise distance) between 2 sequences in an
alignment using the Jukes-Cantor 1 parameter model.
Returns : ArrayRef of all pairwise distances of all sequence pairs in the alignment
Args : Bio::Align::AlignI of DNA sequences
double - gap penalty
Title : D_F81
Usage : my $d = $stat->D_F81($aln)
Function: Calculates D (pairwise distance) between 2 sequences in an
alignment using the Felsenstein 1981 distance model.
Returns : ArrayRef of a 2d array of all pairwise distances in the alignment
Args : Bio::Align::AlignI of DNA sequences
Title : D_Kimura
Usage : my $d = $stat->D_Kimura($aln)
Function: Calculates D (pairwise distance) between 2 sequences in an
alignment using the Kimura 2 parameter model.
Returns : ArrayRef of pairwise distances between all sequences in alignment
Args : Bio::Align::AlignI of DNA sequences
Title : D_Tamura Usage : Function: Returns : Args :
Title : D_F84
Usage : my $d = $stat->D_F84($aln)
Function: Calculates D (pairwise distance) between 2 sequences in an
alignment using the Felsenstein 1984 distance model.
Returns : Distance value
Args : Bio::Align::AlignI of DNA sequences
double - gap penalty
Title : D_TajimaNei
Usage : my $d = $stat->D_TajimaNei($aln)
Function: Calculates D (pairwise distance) between 2 sequences in an
alignment using the TajimaNei 1984 distance model.
Returns : Distance value
Args : Bio::Align::AlignI of DNA sequences
Title : K_JukesCantor
Usage : my $k = $stats->K_JukesCantor($aln)
Function: Calculates K - the number of nucleotide substitutions between
2 seqs - according to the Jukes-Cantor 1 parameter model
This only involves the number of changes between two sequences.
Returns : double
Args : Bio::Align::AlignI
Title : K_TajimaNei
Usage : my $k = $stats->K_TajimaNei($aln)
Function: Calculates K - the number of nucleotide substitutions between
2 seqs - according to the Kimura 2 parameter model.
This does not assume equal frequencies among all the nucleotides.
Returns : ArrayRef of 2d matrix which contains pairwise K values for
all sequences in the alignment
Args : Bio::Align::AlignI
Title : transversions
Usage : my $transversions = $stats->transversion($aln);
Function: Calculates the number of transversions between two sequences in
an alignment
Returns : integer
Args : Bio::Align::AlignI
Title : transitions Usage : my $transitions = Bio::Align::DNAStatistics->transitions($aln); Function: Calculates the number of transitions in a given DNA alignment Returns : integer representing the number of transitions Args : Bio::Align::AlignI object
Title : pairwise_stats Usage : $obj->pairwise_stats($newval) Function: Returns : value of pairwise_stats Args : newvalue (optional)
