Ewan Birney


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


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


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


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


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 email or the web:


AUTHORS - Heikki Lehvaslaiho

Email: heikki@ebi.ac.uk


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.

           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    : 


 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