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Bio::AlignIO::po.3pm

NAME

Bio::AlignIO::po - po MSA Sequence input/output stream

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 'po' format flat file databases. 'po' format is the native format of the POA alignment program (Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs', Bioinformatics (2002), 18(3):452-64).

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:

   http://bugzilla.open-bio.org/
 
 

AUTHORS - Matthew Betts

Email: matthew.betts@ii.uib.no

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 : L<Bio::Align::AlignI> object - returns undef on end of file
             or on error
  Args    : NONE
 
 

write_aln

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