Bio::AlignIO::mega - Parse and Create MEGA format data files


    use Bio::AlignIO;
    my $alignio = Bio::AlignIO->new(-format => 'mega',
                                   -file   => 't/data/hemoglobinA.meg');

    while( my $aln = $alignio->next_aln ) {
    # process each alignment or convert to another format like NEXUS


This object handles reading and writing data streams in the MEGA format (Kumar and Nei).


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


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

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 of the bugs and their resolution. Bug reports can be submitted the web:

AUTHOR - Jason Stajich



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.
           Supports the following MEGA format features:
           - The file has to start with '#mega'
           - Reads in the name of the alignment from a comment
             (anything after '!TITLE: ') .
           - Reads in the format parameters datatype

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