debian man page for bio::alignio::mega

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

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-l@bioperl.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-l@bioperl.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:

	 https://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02						   Bio::AlignIO::mega(3pm)