---
name: "Bio::AlignIO::nexus"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::nexus"
---

# Bio::AlignIO::nexus(3pm)

NEXUS format sequence input/output stream

## 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)
```