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.

Mailing Lists
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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ 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 _

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 0 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 emboss format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object