Bio::AlignIO::maf(3) Multiple Alignment Format sequence input stream


Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');
while(my $aln = $alignio->next_aln()){
my $match_line = $aln->match_line;
print $aln, "\n";
print $aln->length, "\n";
print $aln->num_residues, "\n";
print $aln->is_flush, "\n";
print $aln->num_sequences, "\n";
print $aln->consensus_string(60), "\n";
print $aln->get_seq_by_pos(1)->seq, "\n";
print $aln->match_line(), "\n";
print "\n";


This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file.

Writing in MAF format is currently unimplemented.

Spec of MAF format is here:



Please direct usage questions or support issues to the mailing list:

[email protected]

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:

AUTHORS - Allen Day

Email: [email protected]


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $alignio = Bio::AlignIO->new(-format => 'maf'
                                          -file   => '>file',
                                          -idlength => 10,
                                          -idlinebreak => 1);
 Function: Initialize a new L<Bio::AlignIO::maf> reader
 Returns : L<Bio::AlignIO> object
 Args    :


 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
           Throws an exception if trying to read in PHYLIP
           sequential format.
 Returns : L<Bio::SimpleAlign> object
 Args    :