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Bio::Align::DNAStatistUser3Contributed Perl DocumeBio::Align::DNAStatistics(3)

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

SYNOPSIS
	 use Bio::AlignIO;
	 use Bio::Align::DNAStatistics;

	 my $stats = Bio::Align::DNAStatistics->new();
	 my $alignin = Bio::AlignIO->new(-format => 'emboss',
					-file	=> 't/data/insulin.water');
	 my $aln = $alignin->next_aln;
	 my $jcmatrix =	$stats->distance(-align	=> $aln,
					 -method => 'Jukes-Cantor');

	 print $jcmatrix->print_matrix;
	 ## and	for measurements of synonymous /nonsynonymous substitutions ##

	 my $in	= Bio::AlignIO->new(-format => 'fasta',
				   -file   => 't/data/nei_gojobori_test.aln');
	 my $alnobj = $in->next_aln;
	 my ($seq1id,$seq2id) =	map { $_->display_id } $alnobj->each_seq;
	 my $results = $stats->calc_KaKs_pair($alnobj, $seq1id,	$seq2id);
	 print "comparing ".$results->[0]{'Seq1'}." and	".$results->[0]{'Seq2'}."\n";
	 for (sort keys	%{$results->[0]} ){
	     next if /Seq/;
	     printf("%-9s %.4f \n",$_ ,	$results->[0]{$_});
	 }

	 my $results2 =	$stats->calc_all_KaKs_pairs($alnobj);
	 for my	$an (@$results2){
	     print "comparing ". $an->{'Seq1'}." and ".	$an->{'Seq2'}. " \n";
	     for (sort keys %$an ){
		 next if /Seq/;
		 printf("%-9s %.4f \n",$_ , $an->{$_});
	     }
	     print "\n\n";
	 }

	 my $result3 = $stats->calc_average_KaKs($alnobj, 1000);
	 for (sort keys	%$result3 ){
	     next if /Seq/;
	     printf("%-9s %.4f \n",$_ ,	$result3->{$_});
	 }

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.

       Several different distance method calculations are supported.  Listed
       in brackets are the pattern which will match

       o  JukesCantor [jc|jukes|jukescantor|jukes-cantor]

       o  Uncorrected [jcuncor|uncorrected]

       o  F81 [f81|felsenstein]

       o  Kimura [k2|k2p|k80|kimura]

       o  Tamura [t92|tamura|tamura92]

       o  F84 [f84|felsenstein84]

       o  TajimaNei [tajimanei|tajima\-nei]

       o  JinNei [jinnei|jin\-nei] (not	implemented)

       There are also three methods to calculate the ratio of synonymous to
       non-synonymous mutations.  All are implementations of the Nei-Gojobori
       evolutionary pathway method and use the Jukes-Cantor method of
       nucleotide substitution.	This method works well so long as the
       nucleotide frequencies are roughly equal	and there is no	significant
       transition/transversion bias.  In order to use these methods there are
       several pre-requisites for the alignment.

       1. DNA alignment	must be	based on protein alignment. Use	the subroutine
	  "aa_to_dna_aln" in Bio::Align::Utilities to achieve this.

       2. Therefore alignment gaps must	be in multiples	of 3 (representing an
	  aa deletion/insertion) and at	present	must be	indicated by a '-'
	  symbol.

       3. Alignment must be solely of coding region and	be in reading frame 0
	  to achieve meaningful	results

       4. Alignment must therefore be a	multiple of 3 nucleotides long.

       5. All sequences	must be	the same length	(including gaps). This should
	  be the case anyway if	the sequences have been	automatically aligned
	  using	a program like Clustal.

       6. Only the standard codon alphabet is supported	at present.

       calc_KaKs_pair()	calculates a number of statistics for a	named pair of
       sequences in the	alignment.

       calc_all_KaKs_pairs() calculates	these statistics for all pairwise
       comparisons in an MSA.  The statistics returned are:

       o  S_d -	Number of synonymous mutations between the 2 sequences.

       o  N_d -	Number of non-synonymous mutations between the 2 sequences.

       o  S -  Mean number of  synonymous sites	in both	sequences.

       o  N -  mean number of  synonymous sites	in both	sequences.

       o  P_s -	proportion of synonymous differences in	both sequences given
	  by P_s = S_d/S.

       o  P_n -	proportion of non-synonymous differences in both sequences
	  given	by P_n = S_n/S.

       o  D_s -	estimation of synonymous mutations per synonymous site (by
	  Jukes-Cantor).

       o  D_n -	estimation of non-synonymous mutations per non-synonymous site
	  (by Jukes-Cantor).

       o  D_n_var - estimation of variance of D_n .

       o  D_s_var - estimation of variance of S_n.

       o  z_value - calculation	of z value.Positive value indicates D_n	> D_s,
	  negative value indicates D_s > D_n.

       The statistics returned by calc_average_KaKs are:

       o  D_s -	Average	number of synonymous mutations/synonymous site.

       o  D_n -	Average	number of non-synonymous mutations/non-synonymous
	  site.

       o  D_s_var - Estimated variance of Ds from bootstrapped alignments.

       o  D_n_var - Estimated variance of Dn from bootstrapped alignments.

       o  z_score - calculation	of z value. Positive value indicates D_n >D_s,
	  negative values vice versa.

       The design of the code is based around the explanation of the Nei-
       Gojobori	algorithm in the excellent book	"Molecular Evolution and
       Phylogenetics" by Nei and Kumar,	published by Oxford University Press.
       The methods have	been tested using the worked example 4.1 in the	book,
       and reproduce those results. If people like having this sort of
       analysis	in BioPerl other methods for estimating	Ds and Dn can be
       provided	later.

       Much of the DNA distance	code is	based on implementations in EMBOSS
       (Rice et	al, www.emboss.org) [distmat.c]	and PHYLIP (J. Felsenstein et
       al) [dnadist.c].	 Insight also gained from Eddy,	Durbin,	Krogh, &
       Mitchison.

REFERENCES
       o  D_JukesCantor

	  "Phylogenetic	Inference", Swoffrod, Olsen, Waddell and Hillis, in
	  Mol. Systematics, 2nd	ed, 1996, Ch 11.  Derived from "Evolution of
	  Protein Molecules", Jukes & Cantor, in Mammalian Prot. Metab., III,
	  1969,	pp. 21-132.

       o  D_Tamura

	  K Tamura, Mol. Biol. Evol. 1992, 9, 678.

       o  D_Kimura

	  M Kimura, J. Mol. Evol., 1980, 16, 111.

       o  JinNei

	  Jin and Nei, Mol. Biol. Evol.	82, 7, 1990.

       o  D_TajimaNei

	  Tajima and Nei, Mol. Biol. Evol. 1984, 1, 269.

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/wiki/Mailing_lists	- About	the mailing lists

   Support
       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.

   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 the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich
       Email jason-AT-bioperl.org

CONTRIBUTORS
       Richard Adams, richard.adams@ed.ac.uk

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 = Bio::Align::DNAStatistics->new();
	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	: L<Bio::Matrix::PhylipDist> object
	Args	: -align  => Bio::Align::AlignI	object
		  -method => String specifying specific	distance method
			     (implementing class may assume a default)
       See also: L<Bio::Matrix::PhylipDist>

   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	: L<Bio::Matrix::PhylipDist>
	Args	: L<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.
		  Relaxes the assumption of equal base frequencies that	is
		  in JC.
	Returns	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	of DNA sequences

   D_Uncorrected
	Title	: D_Uncorrected
	Usage	: my $d	= $stats->D_Uncorrected($aln)
	Function: Calculate a distance D, no correction	for multiple substitutions
		  is used.  In rare cases where	sequences may not overlap, 'NA'	is
		  substituted for the distance.
	Returns	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	(DNA Alignment)
		  [optional] gap penalty

   D_Kimura
	Title	: D_Kimura
	Usage	: my $d	= $stat->D_Kimura($aln)
	Function: Calculates D (pairwise distance) between all pairs of	sequences
		  in an	alignment using	the Kimura 2 parameter model.
	Returns	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	of DNA sequences

   D_Kimura_variance
	Title	: D_Kimura
	Usage	: my $d	= $stat->D_Kimura_variance($aln)
	Function: Calculates D (pairwise distance) between all pairs of	sequences
		  in an	alignment using	the Kimura 2 parameter model.
	Returns	: array	of 2 L<Bio::Matrix::PhylipDist>,
		  the first is the Kimura distance and the second is
		  a matrix of variance V(K)
	Args	: L<Bio::Align::AlignI>	of DNA sequences

   D_Tamura
	Title	: D_Tamura
	Usage	: Calculates D (pairwise distance) between 2 sequences in an
		  alignment using Tamura 1992 distance model.
	Returns	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	of DNA sequences

   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	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	of DNA sequences
		  [optional] 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	: L<Bio::Matrix::PhylipDist>
	Args	: Bio::Align::AlignI of	DNA sequences

   D_JinNei
	Title	: D_JinNei
	Usage	: my $d	= $stat->D_JinNei($aln)
	Function: Calculates D (pairwise distance) between 2 sequences in an
		  alignment using the Jin-Nei 1990 distance model.
	Returns	: L<Bio::Matrix::PhylipDist>
	Args	: L<Bio::Align::AlignI>	of DNA sequences

   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)

   calc_KaKs_pair
	Title	 : calc_KaKs_pair
	Useage	 : my $results = $stats->calc_KaKs_pair($alnobj,
		   $name1, $name2).
	Function : calculates Nei-Gojobori statistics for pairwise
		   comparison.
	Args	 : A Bio::Align::AlignI	compliant object such as a
		   Bio::SimpleAlign object, and	2 sequence name	strings.
	Returns	 : a reference to a hash of statistics with keys as
		   listed in Description.

   calc_all_KaKs_pairs
	Title	 : calc_all_KaKs_pairs
	Useage	 : my $results2	= $stats->calc_KaKs_pair($alnobj).
	Function : Calculates Nei_gojobori statistics for all pairwise
		   combinations	in sequence.
	Arguments: A Bio::Align::ALignI	compliant object such as
		   a Bio::SimpleAlign object.
	Returns	 : A reference to an array of hashes of	statistics of
		   all pairwise	comparisons in the alignment.

   calc_average_KaKs
	Title	 : calc_average_KaKs.
	Useage	 : my $res= $stats->calc_average_KaKs($alnobj, 1000).
	Function : calculates Nei_Gojobori stats for average of	all
		   sequences in	the alignment.
	Args	 : A Bio::Align::AlignI	compliant object such as a
		   Bio::SimpleAlign object, number of bootstrap	iterations
		   (default 1000).
	Returns	 : A reference to a hash of statistics as listed in Description.

   get_syn_changes
	Title	: get_syn_changes
	Usage	: Bio::Align::DNAStatitics->get_syn_changes
	Function: Generate a hashref of	all pairwise combinations of codns
		  differing by 1
	Returns	: Symetic matrix using hashes
		  First	key is codon
		  and each codon points	to a hashref of	codons
		  the values of	which describe type of change.
		  my $type = $hash{$codon1}->{$codon2};
		  values are :
		    1	synonymous
		    0	non-syn
		   -1	either codon is	a stop codon
	Args	: none

   dnds_pattern_number
	Title	: dnds_pattern_number
	Usage	: my $patterns = $stats->dnds_pattern_number($alnobj);
	Function: Counts the number of codons with no gaps in the MSA
	Returns	: Number of codons with	no gaps	('patterns' in PAML notation)
	Args	: A Bio::Align::AlignI compliant object	such as	a
		   Bio::SimpleAlign object.

perl v5.24.1			  2017-07-08	  Bio::Align::DNAStatistics(3)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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