---
name: "Bio::AlignIO::nexml"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::nexml"
---

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

NeXML format sequence alignment input/output stream driver

## NAME

Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver

## SYNOPSIS

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

## DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from NeXML format. For more information on NeXML, visit \<http://www.nexml.org\>.

## 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

Chase Miller

## CONTRIBUTORS

Mark Jensen, maj@fortinbras.us Rutger Vos, rutgeraldo@gmail.com

## APPENDIX

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

### next\_aln

```
 Title   : next_aln
 Usage   : $aln = $stream->next_aln
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
                or on error
 Args    :
```

See Bio::Align::AlignI

### rewind

```
 Title   : rewind
 Usage   : $alnio->rewind
 Function: Resets the stream
 Returns : none
 Args    : none
```

### doc

```
 Title   : doc
 Usage   : $treeio->doc
 Function: Returns the biophylo nexml document object
 Returns : Bio::Phylo::Project
 Args    : none or Bio::Phylo::Project object
```

### write\_aln

```
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in nexml format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
```

See Bio::Align::AlignI