/ 
bioperl-1.2.2
/ Bio::Align::DNAStatistics

NAME

Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment

SYNOPSIS

    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";
    }

DESCRIPTION

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.

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/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = new Bio::Align::DNAStatistics();
Function: Builds a new Bio::Align::DNAStatistics object 
Returns : Bio::Align::DNAStatistics
Args    : none

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 : Array ref
 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_JukesCantor

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

D_F81

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

D_Kimura

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

D_Tamura

Title   : D_Tamura
Usage   :
Function:
Returns : 
Args    :

D_F84

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

D_TajimaNei

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

K - sequence substitution methods

K_JukesCantor

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

K_TajimaNei

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

transversions

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

transitions

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

Data Methods

pairwise_stats

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