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Bio::Align::Utilities(User Contributed Perl DocumentatBio::Align::Utilities(3)

NAME
       Bio::Align::Utilities - A collection of utilities regarding converting
       and manipulating	alignment objects

SYNOPSIS
	 use Bio::Align::Utilities qw(:all);

	 # Even	if the protein alignments are local make sure the start/end
	 # stored in the LocatableSeq objects are to the full length protein.
	 # The coding sequence that is passed in should	still be the full
	 # length CDS as the nt	alignment will be generated.
	 # %dnaseqs is a hash of CDS sequences (spliced)
	 my $dna_aln = aa_to_dna_aln($aa_aln,\%dnaseqs);

	 # The reverse,	which is simpler. The input alignment has to be
	 # translate-able, with	gap lengths and	an overall length divisible by 3
	 my $aa_aln = dna_to_aa_aln($dna_al);

	 # Generate bootstraps
	 my $replicates	= bootstrap_replicates($aln,$count);

DESCRIPTION
       This module contains utility methods for	manipulating sequence
       alignments (Bio::Align::AlignI) objects.

       The aa_to_dna_aln utility is essentially	the same as the	mrtrans
       program by Bill Pearson available at
       ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar.  Of	course this is
       a pure-Perl implementation, but just to mention that if anything	seems
       odd you can check the alignments	generated against Bill's program.

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-dot-org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   aa_to_dna_aln
	Title	: aa_to_dna_aln
	Usage	: my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs);
	Function: Will convert an AA alignment to DNA space given the
		  corresponding	DNA sequences.	Note that this method expects
		  the DNA sequences to be in frame +1 (GFF frame 0) as it will
		  start	to project into	coordinates starting at	the first base of
		  the DNA sequence, if this alignment represents a different
		  frame	for the	cDNA you will need to edit the DNA sequences
		  to remove the	1st or 2nd bases (and revcom if	things should be).
	Returns	: Bio::Align::AlignI object
	Args	: 2 arguments, the alignment and a hashref.
		  Alignment is a Bio::Align::AlignI of amino acid sequences.
		  The hash reference should have keys which are
		  the display_ids for the aa
		  sequences in the alignment and the values are	a
		  Bio::PrimarySeqI object for the corresponding
		  spliced cDNA sequence.

       See also: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq

   dna_to_aa_aln
	Title	: dna_to_aa_aln
	Usage	: my $aa_aln = dna_to_aa_aln($dna_aln);
	Function: Convert a DNA	alignment to an	amino acid alignment where
		  the length of	all alignment strings and the lengths of any
		  gaps must be divisible by 3
	Returns	: Bio::Align::AlignI object
	Args	: the DNA alignment, a Bio::Align::AlignI of DNA sequences

       See also: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq

   bootstrap_replicates
	Title	: bootstrap_replicates
	Usage	: my $alns = &bootstrap_replicates($aln,100);
	Function: Generate a pseudo-replicate of the data by randomly
		  sampling, with replacement, the columns from an alignment for
		  the non-parametric bootstrap.
	Returns	: Arrayref of L<Bio::SimpleAlign> objects
	Args	: L<Bio::SimpleAlign> object
		  Number of replicates to generate

   bootstrap_replicates_codons
	Title	: bootstrap_replicates_codons
	Usage	: my $alns = &bootstrap_replicates_codons($aln,100);
	Function: Generate a pseudo-replicate of the data by randomly
		  sampling, with replacement, the columns from a codon alignment for
		  the non-parametric bootstrap.	The alignment is assumed to start on
		  the first position of	a codon.
	Returns	: Arrayref of L<Bio::SimpleAlign> objects
	Args	: L<Bio::SimpleAlign> object
		  Number of replicates to generate

   cat
	Title	  : cat
	Usage	  : $aln123 = cat($aln1, $aln2,	$aln3)
	Function  : Concatenates alignment objects. Sequences are identified by	id.
		    An error will be thrown if the sequence ids	are not	unique in the
		    first alignment. If	any ids	are not	present	or not unique in any
		    of the additional alignments then those sequences are omitted from
		    the	concatenated alignment,	and a warning is issued. An error will
		    be thrown if any of	the alignments are not flush, since
		    concatenating such alignments is unlikely to make biological
		    sense.
	Returns	  : A new Bio::SimpleAlign object
	Args	  : A list of Bio::SimpleAlign objects

   most_common_sequences
	Title	  : most_common_sequences
	Usage	  : @common = most_common_sequences ($align, $case_sensitivity)
	Function  : Returns an array of	the sequences that appear most often in	the
		    alignment (although	this probably makes more sense when there is
		    only a single most common sequence).  Sequences are	compared after
		    removing any "-" (gap characters), and ambiguous units (e.g., R
		    for	purines) are only compared to themselves.  The returned
		    sequence is	also missing the "-" since they	don't actually make
		    part of the	sequence.
	Returns	  : Array of text strings.
	Arguments : Optional argument defining whether the comparison between sequences
		    to find the	most common should be case sensitive. Defaults to
		    false, i.e,	not case sensitive.

perl v5.32.1			  2019-12-07	      Bio::Align::Utilities(3)

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

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