NAME

       Bio::AlignIO::nexus - NEXUS format sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

           use Bio::AlignIO;

           my $in = Bio::AlignIO->new(-format => 'nexus',
                                     -file   => 'aln.nexus');
           while( my $aln = $in->next_aln ) {
               # do something with the alignment
           }

DESCRIPTION

       This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See
       method documentation for supported NEXUS features.

ACKNOWLEDGEMENTS

       Will Fisher has written an excellent standalone NEXUS format parser in Perl, readnexus. A
       number of tricks were adapted from it.

FEEDBACK

   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

AUTHORS - Heikki Lehvaslaiho

       Email: heikki-at-bioperl-dot-org

APPENDIX

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

   new
        Title   : new
        Usage   : $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename');
        Function: returns a new Bio::AlignIO object to handle clustalw files
        Returns : Bio::AlignIO::clustalw object
        Args    : -verbose => verbosity setting (-1,0,1,2)
                  -file    => name of file to read in or with ">" - writeout
                  -fh      => alternative to -file param - provide a filehandle
                              to read from/write to
                  -format  => type of Alignment Format to process or produce

                  Customization of nexus flavor output

                  -show_symbols => print the symbols="ATGC" in the data definition
                                   (MrBayes does not like this)
                                   boolean [default is 1]
                  -show_endblock => print an 'endblock;' at the end of the data
                                   (MyBayes does not like this)
                                   boolean [default is 1]

   next_aln
        Title   : next_aln
        Usage   : $aln = $stream->next_aln()
        Function: Returns the next alignment in the stream.

                  Supports the following NEXUS format features:
                  - The file has to start with '#NEXUS'
                  - Reads in the name of the alignment from a comment
                    (anything after 'TITLE: ') .
                  - Sequence names can be given in a taxa block, too.
                  - If matchchar notation is used, converts
                    them back to sequence characters.
                  - Does character conversions specified in the
                    NEXUS equate command.
                  - Sequence names of type 'Homo sapiens' and
                    Homo_sapiens are treated identically.

        Returns : L<Bio::Align::AlignI> object
        Args    :

   write_aln
        Title   : write_aln
        Usage   : $stream->write_aln(@aln)
        Function: Writes the $aln object into the stream in interleaved NEXUS
                  format. Everything is written into a data block.
                  SimpleAlign methods match_char, missing_char and gap_char must be set
                  if you want to see them in the output.
        Returns : 1 for success and 0 for error
        Args    : L<Bio::Align::AlignI> object

   flag
        Title   : flag
        Usage   : $obj->flag($name,$value)
        Function: Get/Set a flag value
        Returns : value of flag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)