Ewan Birney


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 = new Bio::AlignIO(-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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AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here


Additional contributors names and emails here


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