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.