Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SimpleAlign - Multiple alignments held as a set of sequences

SYNOPSIS

         # Use Bio::AlignIO to read in the alignment
         $str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
         $aln = $str->next_aln();

         # Describe
         print $aln->length;
         print $aln->num_residues;
         print $aln->is_flush;
         print $aln->num_sequences;
         print $aln->score;
         print $aln->percentage_identity;
         print $aln->consensus_string(50);

         # Find the position in the alignment for a sequence location
         $pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;

         # Extract sequences and check values for the alignment column $pos
         foreach $seq ($aln->each_seq) {
             $res = $seq->subseq($pos, $pos);
             $count{$res}++;
         }
         foreach $res (keys %count) {
             printf "Res: %s  Count: %2d\n", $res, $count{$res};
         }

         # Manipulate
         $aln->remove_seq($seq);
         $mini_aln = $aln->slice(20,30);  # get a block of columns
         $mini_aln = $aln->select_noncont(1,3,5,7,11); # select certain sequences
         $new_aln = $aln->remove_columns([20,30]); # remove by position
         $new_aln = $aln->remove_columns(['mismatch']); # remove by property

         # Analyze
         $str = $aln->consensus_string($threshold_percent);
         $str = $aln->match_line();
         $str = $aln->cigar_line();
         $id = $aln->percentage_identity;

         # See the module documentation for details and more methods.

DESCRIPTION

       SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very
       permissive of types (it does not insist on sequences being all same length, for example).
       Think of it as a set of sequences with a whole series of built-in manipulations and
       methods for reading and writing alignments.

       SimpleAlign uses Bio::LocatableSeq, a subclass of Bio::PrimarySeq, to store its sequences.
       These are subsequences with a start and end positions in the parent reference sequence.
       Each sequence in the SimpleAlign object is a Bio::LocatableSeq.

       SimpleAlign expects the combination of name, start, and end for a given sequence to be
       unique in the alignment, and this is the key for the internal hashes (name, start, end are
       abbreviated "nse" in the code).  However, in some cases people do not want the
       name/start-end to be displayed: either multiple names in an alignment or names specific to
       the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called "displayname", and
       generally is what is used to print out the alignment. They default to name/start-end.

       The SimpleAlign Module is derived from the Align module by Ewan Birney.

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 one of the Bioperl mailing lists.  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 the bugs and their
       resolution. Bug reports can be submitted via the web:

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

AUTHOR

       Ewan Birney, birney@ebi.ac.uk

CONTRIBUTORS

       Allen Day, allenday-at-ucla.edu, Richard Adams, Richard.Adams-at-ed.ac.uk, David J. Evans,
       David.Evans-at-vir.gla.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org, Allen Smith,
       allens-at-cpan.org, Jason Stajich, jason-at-bioperl.org, Anthony Underwood,
       aunderwood-at-phls.org.uk, Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu Brian Osborne,
       bosborne at alum.mit.edu Weigang Qiu, Weigang at GENECTR-HUNTER-CUNY-EDU Hongyu Zhang,
       forward at hongyu.org Jay Hannah, jay at jays.net Alexandr Bezginov, albezg at gmail.com

SEE ALSO

       Bio::LocatableSeq

APPENDIX

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

   new
        Title     : new
        Usage     : my $aln = Bio::SimpleAlign->new();
        Function  : Creates a new simple align object
        Returns   : Bio::SimpleAlign
        Args      : -source     => string representing the source program
                                   where this alignment came from
                    -annotation => Bio::AnnotationCollectionI
                    -seq_annotation => Bio::AnnotationCollectionI for sequences (requires -annotation also be set)
                    -seqs       => array ref containing Bio::LocatableSeq or Bio::Seq::Meta
                    -consensus  => consensus string
                    -consensus_meta  => Bio::Seq::Meta object containing consensus met information (kludge)

Modifier methods

       These methods modify the MSA by adding, removing or shuffling complete sequences.

   add_seq
        Title     : add_seq
        Usage     : $myalign->add_seq($newseq);
                    $myalign->add_seq(-SEQ=>$newseq, -ORDER=>5);
        Function  : Adds another sequence to the alignment. *Does not* align
                    it - just adds it to the hashes.
                    If -ORDER is specified, the sequence is inserted at the
                    the position spec'd by -ORDER, and existing sequences
                    are pushed down the storage array.
        Returns   : nothing
        Args      : A Bio::LocatableSeq object
                    Positive integer for the sequence position (optional)

       See Bio::LocatableSeq for more information

   remove_seq
        Title     : remove_seq
        Usage     : $aln->remove_seq($seq);
        Function  : Removes a single sequence from an alignment
        Returns   :
        Argument  : a Bio::LocatableSeq object

   purge
        Title   : purge
        Usage   : $aln->purge(0.7);
        Function: Removes sequences above given sequence similarity
                  This function will grind on large alignments. Beware!
        Example :
        Returns : An array of the removed sequences
        Args    : float, threshold for similarity

   sort_alphabetically
        Title     : sort_alphabetically
        Usage     : $ali->sort_alphabetically
        Function  : Changes the order of the alignment to alphabetical on name
                    followed by numerical by number.
        Returns   :
        Argument  :

   sort_by_list
        Title     : sort_by_list
        Usage     : $aln_ordered=$aln->sort_by_list($list_file)
        Function  : Arbitrarily order sequences in an alignment
        Returns   : A new Bio::SimpleAlign object
        Argument  : a file listing sequence names in intended order (one name per line)

   set_new_reference
        Title     : set_new_reference
        Usage     : $aln->set_new_reference(3 or 'B31'):  Select the 3rd sequence, or
                    the sequence whoes name is "B31" (full, exact, and case-sensitive),
                    as the reference (1st) sequence
        Function  : Change/Set a new reference (i.e., the first) sequence
        Returns   : a new Bio::SimpleAlign object.
                    Throws an exception if designated sequence not found
        Argument  : a positive integer of sequence order, or a sequence name
                    in the original alignment

   uniq_seq
        Title     : uniq_seq
        Usage     : $aln->uniq_seq():  Remove identical sequences in
                    in the alignment.  Ambiguous base ("N", "n") and
                    leading and ending gaps ("-") are NOT counted as
                    differences.
        Function  : Make a new alignment of unique sequence types (STs)
        Returns   : 1a. if called in a scalar context,
                       a new Bio::SimpleAlign object (all sequences renamed as "ST")
                    1b. if called in an array context,
                       a new Bio::SimpleAlign object, and a hashref whose keys
                       are sequence types, and whose values are arrayrefs to
                       lists of sequence ids within the corresponding sequence type
                    2. if $aln->verbose > 0, ST of each sequence is sent to
                       STDERR (in a tabular format)
        Argument  : None

Sequence selection methods

       Methods returning one or more sequences objects.

   each_seq
        Title     : each_seq
        Usage     : foreach $seq ( $align->each_seq() )
        Function  : Gets a Seq object from the alignment
        Returns   : Seq object
        Argument  :

   each_alphabetically
        Title     : each_alphabetically
        Usage     : foreach $seq ( $ali->each_alphabetically() )
        Function  : Returns a sequence object, but the objects are returned
                    in alphabetically sorted order.
                    Does not change the order of the alignment.
        Returns   : Seq object
        Argument  :

   each_seq_with_id
        Title     : each_seq_with_id
        Usage     : foreach $seq ( $align->each_seq_with_id() )
        Function  : Gets a Seq objects from the alignment, the contents
                    being those sequences with the given name (there may be
                    more than one)
        Returns   : Seq object
        Argument  : a seq name

   get_seq_by_pos
        Title     : get_seq_by_pos
        Usage     : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment
        Function  : Gets a sequence based on its position in the alignment.
                    Numbering starts from 1.  Sequence positions larger than
                    num_sequences() will throw an error.
        Returns   : a Bio::LocatableSeq object
        Args      : positive integer for the sequence position

   get_seq_by_id
        Title     : get_seq_by_id
        Usage     : $seq = $aln->get_seq_by_id($name) # seq named $name
        Function  : Gets a sequence based on its name.
                    Sequences that do not exist will warn and return undef
        Returns   : a Bio::LocatableSeq object
        Args      : string for sequence name

   seq_with_features
        Title   : seq_with_features
        Usage   : $seq = $aln->seq_with_features(-pos => 1,
                                                 -consensus => 60
                                                 -mask =>
                  sub { my $consensus = shift;

                        for my $i (1..5){
                           my $n = 'N' x $i;
                           my $q = '\?' x $i;
                           while($consensus =~ /[^?]$q[^?]/){
                              $consensus =~ s/([^?])$q([^?])/$1$n$2/;
                           }
                         }
                        return $consensus;
                      }
                                                );
        Function: produces a Bio::Seq object by first splicing gaps from -pos
                  (by means of a splice_by_seq_pos() call), then creating
                  features using non-? chars (by means of a consensus_string()
                  call with stringency -consensus).
        Returns : a Bio::Seq object
        Args    : -pos : required. sequence from which to build the Bio::Seq
                    object
                  -consensus : optional, defaults to consensus_string()'s
                    default cutoff value
                  -mask : optional, a coderef to apply to consensus_string()'s
                    output before building features.  this may be useful for
                    closing gaps of 1 bp by masking over them with N, for
                    instance

Create new alignments

       The result of these methods are horizontal or vertical subsets of the current MSA.

   select
        Title     : select
        Usage     : $aln2 = $aln->select(1, 3) # three first sequences
        Function  : Creates a new alignment from a continuous subset of
                    sequences.  Numbering starts from 1.  Sequence positions
                    larger than num_sequences() will throw an error.
        Returns   : a Bio::SimpleAlign object
        Args      : positive integer for the first sequence
                    positive integer for the last sequence to include (optional)

   select_noncont
        Title     : select_noncont
        Usage     : # 1st and 3rd sequences, sorted
                    $aln2 = $aln->select_noncont(1, 3)

                    # 1st and 3rd sequences, sorted (same as first)
                    $aln2 = $aln->select_noncont(3, 1)

                    # 1st and 3rd sequences, unsorted
                    $aln2 = $aln->select_noncont('nosort',3, 1)

        Function  : Creates a new alignment from a subset of sequences.  Numbering
                    starts from 1.  Sequence positions larger than num_sequences() will
                    throw an error.  Sorts the order added to new alignment by default,
                    to prevent sorting pass 'nosort' as the first argument in the list.
        Returns   : a Bio::SimpleAlign object
        Args      : array of integers for the sequences.  If the string 'nosort' is
                    passed as the first argument, the sequences will not be sorted
                    in the new alignment but will appear in the order listed.

   select_noncont_by_name
        Title     : select_noncont_by_name
        Usage     : my $aln2 = $aln->select_noncont_by_name('A123', 'B456');
        Function  : Creates a new alignment from a subset of sequences which are
                    selected by name (sequence ID).
        Returns   : a Bio::SimpleAlign object
        Args      : array of names (i.e., identifiers) for the sequences.

   slice
        Title     : slice
        Usage     : $aln2 = $aln->slice(20,30)
        Function  : Creates a slice from the alignment inclusive of start and
                    end columns, and the first column in the alignment is denoted 1.
                    Sequences with no residues in the slice are excluded from the
                    new alignment and a warning is printed. Slice beyond the length of
                    the sequence does not do padding.
        Returns   : A Bio::SimpleAlign object
        Args      : Positive integer for start column, positive integer for end column,
                    optional boolean which if true will keep gap-only columns in the newly
                    created slice. Example:

                    $aln2 = $aln->slice(20,30,1)

   remove_columns
        Title     : remove_columns
        Usage     : $aln2 = $aln->remove_columns(['mismatch','weak']) or
                    $aln2 = $aln->remove_columns([0,0],[6,8])
        Function  : Creates an aligment with columns removed corresponding to
                    the specified type or by specifying the columns by number.
        Returns   : Bio::SimpleAlign object
        Args      : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'|
                    'all_gaps_columns') or array ref where the referenced array
                    contains a pair of integers that specify a range.
                    The first column is 0

   remove_gaps
        Title     : remove_gaps
        Usage     : $aln2 = $aln->remove_gaps
        Function  : Creates an aligment with gaps removed
        Returns   : a Bio::SimpleAlign object
        Args      : a gap character(optional) if none specified taken
                       from $self->gap_char,
                    [optional] $all_gaps_columns flag (1 or 0, default is 0)
                               indicates that only all-gaps columns should be deleted

       Used from method remove_columns in most cases. Set gap character using gap_char().

Change sequences within the MSA

       These methods affect characters in all sequences without changing the alignment.

   splice_by_seq_pos
        Title   : splice_by_seq_pos
        Usage   : $status = splice_by_seq_pos(1);
        Function: splices all aligned sequences where the specified sequence
                  has gaps.
        Example :
        Returns : 1 on success
        Args    : position of sequence to splice by

   map_chars
        Title     : map_chars
        Usage     : $ali->map_chars('\.','-')
        Function  : Does a s/$arg1/$arg2/ on the sequences. Useful for gap
                    characters.

                    Note that the first argument is interpreted as a regexp
                    so be careful and escape any wild card characters (e.g.
                    do $ali->map_chars('\.','-') to replace periods with dashes.
        Returns   : 1 on success
        Argument  : A regexp and a string

   uppercase
        Title     : uppercase()
        Usage     : $ali->uppercase()
        Function  : Sets all the sequences to uppercase
        Returns   : 1 on success
        Argument  :

   cigar_line
        Title    : cigar_line()
        Usage    : %cigars = $align->cigar_line()
        Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment
                   Report) line for each sequence in the alignment. Examples are
                   "1,60" or "5,10:12,58", where the numbers refer to conserved
                   positions within the alignment. The keys of the hash are the
                   NSEs (name/start/end) assigned to each sequence.
        Args     : threshold (optional, defaults to 100)
        Returns  : Hash of strings (cigar lines)

   match_line
        Title    : match_line()
        Usage    : $line = $align->match_line()
        Function : Generates a match line - much like consensus string
                   except that a line indicating the '*' for a match.
        Args     : (optional) Match line characters ('*' by default)
                   (optional) Strong match char (':' by default)
                   (optional) Weak match char ('.' by default)
        Returns  : String

   gap_line
        Title    : gap_line()
        Usage    : $line = $align->gap_line()
        Function : Generates a gap line - much like consensus string
                   except that a line where '-' represents gap
        Args     : (optional) gap line characters ('-' by default)
        Returns  : string

   all_gap_line
        Title    : all_gap_line()
        Usage    : $line = $align->all_gap_line()
        Function : Generates a gap line - much like consensus string
                   except that a line where '-' represents all-gap column
        Args     : (optional) gap line characters ('-' by default)
        Returns  : string

   gap_col_matrix
        Title    : gap_col_matrix()
        Usage    : my $cols = $align->gap_col_matrix()
        Function : Generates an array where each element in the array is a
                   hash reference with a key of the sequence name and a
                   value of 1 if the sequence has a gap at that column
        Returns  : Reference to an array
        Args     : Optional: gap line character ($aln->gap_char or '-' by default)

   match
        Title     : match()
        Usage     : $ali->match()
        Function  : Goes through all columns and changes residues that are
                    identical to residue in first sequence to match '.'
                    character. Sets match_char.

                    USE WITH CARE: Most MSA formats do not support match
                    characters in sequences, so this is mostly for output
                    only. NEXUS format (Bio::AlignIO::nexus) can handle
                    it.
        Returns   : 1 on success
        Argument  : a match character, optional, defaults to '.'

   unmatch
        Title     : unmatch()
        Usage     : $ali->unmatch()
        Function  : Undoes the effect of method match. Unsets match_char.
        Returns   : 1 on success
        Argument  : a match character, optional, defaults to '.'

       See match and match_char

MSA attributes

       Methods for setting and reading the MSA attributes.

       Note that the methods defining character semantics depend on the user to set them
       sensibly.  They are needed only by certain input/output methods. Unset them by setting to
       an empty string ('').

   id
        Title     : id
        Usage     : $myalign->id("Ig")
        Function  : Gets/sets the id field of the alignment
        Returns   : An id string
        Argument  : An id string (optional)

   accession
        Title     : accession
        Usage     : $myalign->accession("PF00244")
        Function  : Gets/sets the accession field of the alignment
        Returns   : An acc string
        Argument  : An acc string (optional)

   description
        Title     : description
        Usage     : $myalign->description("14-3-3 proteins")
        Function  : Gets/sets the description field of the alignment
        Returns   : An description string
        Argument  : An description string (optional)

   missing_char
        Title     : missing_char
        Usage     : $myalign->missing_char("?")
        Function  : Gets/sets the missing_char attribute of the alignment
                    It is generally recommended to set it to 'n' or 'N'
                    for nucleotides and to 'X' for protein.
        Returns   : An missing_char string,
        Argument  : An missing_char string (optional)

   match_char
        Title     : match_char
        Usage     : $myalign->match_char('.')
        Function  : Gets/sets the match_char attribute of the alignment
        Returns   : An match_char string,
        Argument  : An match_char string (optional)

   gap_char
        Title     : gap_char
        Usage     : $myalign->gap_char('-')
        Function  : Gets/sets the gap_char attribute of the alignment
        Returns   : An gap_char string, defaults to '-'
        Argument  : An gap_char string (optional)

   symbol_chars
        Title   : symbol_chars
        Usage   : my @symbolchars = $aln->symbol_chars;
        Function: Returns all the seen symbols (other than gaps)
        Returns : array of characters that are the seen symbols
        Args    : boolean to include the gap/missing/match characters

Alignment descriptors

       These read only methods describe the MSA in various ways.

   score
        Title     : score
        Usage     : $str = $ali->score()
        Function  : get/set a score of the alignment
        Returns   : a score for the alignment
        Argument  : an optional score to set

   consensus_string
        Title     : consensus_string
        Usage     : $str = $ali->consensus_string($threshold_percent)
        Function  : Makes a strict consensus
        Returns   : Consensus string
        Argument  : Optional threshold ranging from 0 to 100.
                    The consensus residue has to appear at least threshold %
                    of the sequences at a given location, otherwise a '?'
                    character will be placed at that location.
                    (Default value = 0%)

   consensus_conservation
        Title     : consensus_conservation
        Usage     : @conservation = $ali->consensus_conservation();
        Function  : Conservation (as a percent) of each position of alignment
        Returns   : Array of percentages [0-100]. Gap columns are 0% conserved.
        Argument  :

   consensus_iupac
        Title     : consensus_iupac
        Usage     : $str = $ali->consensus_iupac()
        Function  : Makes a consensus using IUPAC ambiguity codes from DNA
                    and RNA. The output is in upper case except when gaps in
                    a column force output to be in lower case.

                    Note that if your alignment sequences contain a lot of
                    IUPAC ambiquity codes you often have to manually set
                    alphabet.  Bio::PrimarySeq::_guess_type thinks they
                    indicate a protein sequence.
        Returns   : consensus string
        Argument  : none
        Throws    : on protein sequences

   consensus_meta
        Title     : consensus_meta
        Usage     : $seqmeta = $ali->consensus_meta()
        Function  : Returns a Bio::Seq::Meta object containing the consensus
                    strings derived from meta data analysis.
        Returns   : Bio::Seq::Meta
        Argument  : Bio::Seq::Meta
        Throws    : non-MetaI object

   is_flush
        Title     : is_flush
        Usage     : if ( $ali->is_flush() )
        Function  : Tells you whether the alignment
                  : is flush, i.e. all of the same length
        Returns   : 1 or 0
        Argument  :

   length
        Title     : length()
        Usage     : $len = $ali->length()
        Function  : Returns the maximum length of the alignment.
                    To be sure the alignment is a block, use is_flush
        Returns   : Integer
        Argument  :

   maxdisplayname_length
        Title     : maxdisplayname_length
        Usage     : $ali->maxdisplayname_length()
        Function  : Gets the maximum length of the displayname in the
                    alignment. Used in writing out various MSA formats.
        Returns   : integer
        Argument  :

   max_metaname_length
        Title     : max_metaname_length
        Usage     : $ali->max_metaname_length()
        Function  : Gets the maximum length of the meta name tags in the
                    alignment for the sequences and for the alignment.
                    Used in writing out various MSA formats.
        Returns   : integer
        Argument  : None

   num_residues
        Title     : num_residues
        Usage     : $no = $ali->num_residues
        Function  : number of residues in total in the alignment
        Returns   : integer
        Argument  :
        Note      : replaces no_residues()

   num_sequences
        Title     : num_sequences
        Usage     : $depth = $ali->num_sequences
        Function  : number of sequence in the sequence alignment
        Returns   : integer
        Argument  : none
        Note      : replaces no_sequences()

   average_percentage_identity
        Title   : average_percentage_identity
        Usage   : $id = $align->average_percentage_identity
        Function: The function uses a fast method to calculate the average
                  percentage identity of the alignment
        Returns : The average percentage identity of the alignment
        Args    : None
        Notes   : This method implemented by Kevin Howe calculates a figure that is
                  designed to be similar to the average pairwise identity of the
                  alignment (identical in the absence of gaps), without having to
                  explicitly calculate pairwise identities proposed by Richard Durbin.
                  Validated by Ewan Birney ad Alex Bateman.

   percentage_identity
        Title   : percentage_identity
        Usage   : $id = $align->percentage_identity
        Function: The function calculates the average percentage identity
                  (aliased to average_percentage_identity)
        Returns : The average percentage identity
        Args    : None

   overall_percentage_identity
        Title   : overall_percentage_identity
        Usage   : $id = $align->overall_percentage_identity
                  $id = $align->overall_percentage_identity('short')
        Function: The function calculates the percentage identity of
                  the conserved columns
        Returns : The percentage identity of the conserved columns
        Args    : length value to use, optional defaults to alignment length
                        possible values: 'align', 'short', 'long'

       The argument values 'short' and 'long' refer to shortest and longest sequence in the
       alignment. Method modification code by Hongyu Zhang.

Alignment positions

       Methods to map a sequence position into an alignment column and back.
       column_from_residue_number() does the former. The latter is really a property of the
       sequence object and can done using Bio::LocatableSeq::location_from_column:

           # select somehow a sequence from the alignment, e.g.
           my $seq = $aln->get_seq_by_pos(1);
           #$loc is undef or Bio::LocationI object
           my $loc = $seq->location_from_column(5);

   column_from_residue_number
        Title   : column_from_residue_number
        Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
        Function: This function gives the position in the alignment
                  (i.e. column number) of the given residue number in the
                  sequence with the given name. For example, for the
                  alignment

                    Seq1/91-97 AC..DEF.GH.
                    Seq2/24-30 ACGG.RTY...
                       Seq3/43-51 AC.DDEF.GHI

                  column_from_residue_number( "Seq1", 94 ) returns 6.
                  column_from_residue_number( "Seq2", 25 ) returns 2.
                  column_from_residue_number( "Seq3", 50 ) returns 10.

                  An exception is thrown if the residue number would lie
                  outside the length of the aligment
                  (e.g. column_from_residue_number( "Seq2", 22 )

                 Note: If the the parent sequence is represented by more than
                       one alignment sequence and the residue number is present in
                       them, this method finds only the first one.

        Returns : A column number for the position in the alignment of the
                  given residue in the given sequence (1 = first column)
        Args    : A sequence id/name (not a name/start-end)
                  A residue number in the whole sequence (not just that
                  segment of it in the alignment)

Sequence names

       Methods to manipulate the display name. The default name based on the sequence id and
       subsequence positions can be overridden in various ways.

   displayname
        Title     : displayname
        Usage     : $myalign->displayname("Ig", "IgA")
        Function  : Gets/sets the display name of a sequence in the alignment
        Returns   : A display name string
        Argument  : name of the sequence
                    displayname of the sequence (optional)

   set_displayname_count
        Title     : set_displayname_count
        Usage     : $ali->set_displayname_count
        Function  : Sets the names to be name_# where # is the number of
                    times this name has been used.
        Returns   : 1, on success
        Argument  :

   set_displayname_flat
        Title     : set_displayname_flat
        Usage     : $ali->set_displayname_flat()
        Function  : Makes all the sequences be displayed as just their name,
                    not name/start-end (NSE)
        Returns   : 1
        Argument  :

   set_displayname_normal
        Title     : set_displayname_normal
        Usage     : $ali->set_displayname_normal()
        Function  : Makes all the sequences be displayed as name/start-end (NSE)
        Returns   : 1, on success
        Argument  :

   source
        Title   : source
        Usage   : $obj->source($newval)
        Function: sets the Alignment source program
        Example :
        Returns : value of source
        Args    : newvalue (optional)

   set_displayname_safe
        Title     : set_displayname_safe
        Usage     : ($new_aln, $ref_name)=$ali->set_displayname_safe(4)
        Function  : Assign machine-generated serial names to sequences in input order.
                    Designed to protect names during PHYLIP runs. Assign 10-char string
                    in the form of "S000000001" to "S999999999". Restore the original
                    names using "restore_displayname".
        Returns   : 1. a new $aln with system names;
                    2. a hash ref for restoring names
        Argument  : Number for id length (default 10)

   restore_displayname
        Title     : restore_displayname
        Usage     : $aln_name_restored=$ali->restore_displayname($hash_ref)
        Function  : Restore original sequence names (after running
                    $ali->set_displayname_safe)
        Returns   : a new $aln with names restored.
        Argument  : a hash reference of names from "set_displayname_safe".

   sort_by_start
        Title     : sort_by_start
        Usage     : $ali->sort_by_start
        Function  : Changes the order of the alignment to the start position of each
                    subalignment
        Returns   : 1 on success
        Argument  :

   bracket_string
        Title     : bracket_string
        Usage     : my @params = (-refseq     => 'testseq',
                                  -allele1    => 'allele1',
                                  -allele2    => 'allele2',
                                  -delimiters => '{}',
                                  -separator  => '/');
                    $str = $aln->bracket_string(@params)

        Function :  When supplied with a list of parameters (see below), returns a
                    string in BIC format. This is used for allelic comparisons.
                    Briefly, if either allele contains a base change when compared to
                    the refseq, the base or gap for each allele is represented in
                    brackets in the order present in the 'alleles' parameter.

                    For the following data:

                    >testseq
                    GGATCCATTGCTACT
                    >allele1
                    GGATCCATTCCTACT
                    >allele2
                    GGAT--ATTCCTCCT

                    the returned string with parameters 'refseq => testseq' and
                    'alleles => [qw(allele1 allele2)]' would be:

                    GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
        Returns   : BIC-formatted string
        Argument  : Required args
                       refseq    : string (ID) of the reference sequence used
                                   as basis for comparison
                       allele1   : string (ID) of the first allele
                       allele2   : string (ID) of the second allele
                    Optional args
                       delimiters: two symbol string of left and right delimiters.
                                   Only the first two symbols are used
                                   default = '[]'
                       separator : string used as a separator.  Only the first
                                   symbol is used
                                   default = '/'
        Throws    : On no refseq/alleles, or invalid refseq/alleles.

   methods implementing Bio::FeatureHolderI
       FeatureHolderI implementation to support labeled character sets like one would get from
       NEXUS represented data.

   get_SeqFeatures
        Usage   : @features = $aln->get_SeqFeatures
        Function: Get the feature objects held by this feature holder.
        Example :
        Returns : an array of Bio::SeqFeatureI implementing objects
        Args    : optional filter coderef, taking a Bio::SeqFeatureI
                : as argument, returning TRUE if wanted, FALSE if
                : unwanted

   add_SeqFeature
        Usage   : $aln->add_SeqFeature($subfeat);
        Function: Adds a SeqFeature into the SeqFeature array. The 'EXPAND' qualifier
                  (see L<Bio::FeatureHolderI>) is supported, but has no effect.
        Example :
        Returns : 1 on success
        Args    : a Bio::SeqFeatureI object

   remove_SeqFeatures
        Usage   : $obj->remove_SeqFeatures
        Function: Removes all SeqFeatures.  If you want to remove only a subset,
                  remove that subset from the returned array, and add back the rest.
        Returns : The array of Bio::SeqFeatureI features that was
                  deleted from this alignment.
        Args    : none

   feature_count
        Title   : feature_count
        Usage   : $obj->feature_count()
        Function: Return the number of SeqFeatures attached to the alignment
        Returns : integer representing the number of SeqFeatures
        Args    : None

   get_all_SeqFeatures
        Title   : get_all_SeqFeatures
        Usage   :
        Function: Get all SeqFeatures.
        Example :
        Returns : an array of Bio::SeqFeatureI implementing objects
        Args    : none
        Note    : Falls through to Bio::FeatureHolderI implementation.

   methods for Bio::AnnotatableI
       AnnotatableI implementation to support sequence alignments which contain annotation
       (NEXUS, Stockholm).

   annotation
        Title   : annotation
        Usage   : $ann = $aln->annotation or
                  $aln->annotation($ann)
        Function: Gets or sets the annotation
        Returns : Bio::AnnotationCollectionI object
        Args    : None or Bio::AnnotationCollectionI object

       See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

Deprecated methods

   no_residues
        Title     : no_residues
        Usage     : $no = $ali->no_residues
        Function  : number of residues in total in the alignment
        Returns   : integer
        Argument  :
        Note      : deprecated in favor of num_residues()

   no_sequences
        Title     : no_sequences
        Usage     : $depth = $ali->no_sequences
        Function  : number of sequence in the sequence alignment
        Returns   : integer
        Argument  :
        Note      : deprecated in favor of num_sequences()

   mask_columns
        Title     : mask_columns
        Usage     : $aln2 = $aln->mask_columns(20,30)
        Function  : Masks a slice of the alignment inclusive of start and
                    end columns, and the first column in the alignment is denoted 1.
                    Mask beyond the length of the sequence does not do padding.
        Returns   : A Bio::SimpleAlign object
        Args      : Positive integer for start column, positive integer for end column,
                    optional string value use for the mask. Example:

                    $aln2 = $aln->mask_columns(20,30,'?')
        Note      : Masking must use a character that is not used for gaps or
                    frameshifts.  These can be adjusted using the relevant global
                    variables, but be aware these may be (uncontrollably) modified
                    elsewhere within BioPerl (see bug 2715)