Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

    # do not use the object directly
    use Bio::AlignIO;
    # read in an alignment from the EMBOSS program water
    my $in = Bio::AlignIO->new(-format => 'emboss',
                              -file   => 'seq.water');
    while( my $aln = $in->next_aln ) {
    # do something with the alignment
    }

This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.

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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.

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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 : L<Bio::Align::AlignI> object - returns 0 on end of file
	    or on error
 Args    : NONE

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