Bio::AlignIO::mega(3)                      User Contributed Perl Documentation




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

SYNOPSIS
           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
           }

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

FEEDBACK
   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.

         bioperl-lATbioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

       bioperl-lATbioperl.org

       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:

         http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

APPENDIX
       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.
                  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

   write_aln
        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



perl v5.12.2                                                 February 24, 2011