Ewan Birney


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


    use Bio::AlignIO;
    my $alignio = new Bio::AlignIO(-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).


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AUTHOR - Jason Stajich

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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.
           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