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

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		 Bio::AlignIO::mega(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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