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Bio::AlignIO::nexml(3pm) User Contributed Perl Documentation Bio::AlignIO::nexml(3pm)


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


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


This object can transform Bio::SimpleAlign objects to and from NeXML format. For more information on NeXML, visit <>.



Please direct usage questions or support issues to the mailing list:

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:


Chase Miller


Mark Jensen, Rutger Vos,


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


 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


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


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


 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

2018-10-27 perl v5.26.2