NAME
Bio::Phylo::Matrices::Alignment - The alignment object to aggregate sequences.
SYNOPSIS
use Bio::Phylo::Matrices::Alignment;
use Bio::Phylo::Matrices::Sequence;
my $alignment = Bio::Phylo::Matrices::Alignment->new;
my $sequence = Bio::Phylo::Matrices::Sequence->new;
$alignment->insert($sequence);DESCRIPTION
This module aggregates sequence objects in a larger container object. The alignment object inherits from the Bio::Phylo::Listable object, so look there for more methods applicable to alignment objects.
METHODS
CONSTRUCTOR
- new()
-
Type : Constructor Title : new Usage : my $alignment = Bio::Phylo::Matrices::Alignment->new; Function: Instantiates a Bio::Phylo::Matrices::Alignment object. Returns : A Bio::Phylo::Matrices::Alignment object. Args : NONE required.
SEE ALSO
- Bio::Phylo::Listable
-
This object inherits from Bio::Phylo::Listable, so the methods defined therein are also applicable to Bio::Phylo::Matrices::Alignment objects.
- Bio::Phylo::Manual
-
Also see the manual: Bio::Phylo::Manual.
FORUM
CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo
BUGS
Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:
$Id: Alignment.pm,v 1.8 2005/09/29 20:31:17 rvosa Exp $
AUTHOR
Rutger A. Vos,
- email:
rvosa@sfu.ca - web page: http://www.sfu.ca/~rvosa/
ACKNOWLEDGEMENTS
The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.
COPYRIGHT & LICENSE
Copyright 2005 Rutger A. Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.