NAME

Bio::Phylo::Unparsers::Nexus - Unparses nexus matrices. No serviceable parts inside.

DESCRIPTION

This module turns a Bio::Phylo::Matrices::Matrix object into a nexus formatted matrix. It is called by the Bio::Phylo::IO facade, don't call it directly. You can pass the following additional arguments to the unparse call:

# an array reference of matrix, forest and taxa objects:
-phylo => [ $block1, $block2 ]

# the arguments that can be passed for matrix objects, 
# refer to Bio::Phylo::Matrices::Matrix::to_nexus:
-matrix_args => {}

# the arguments that can be passed for forest objects, 
# refer to Bio::Phylo::Forest::to_nexus:
-forest_args => {}

# the arguments that can be passed for taxa objects, 
# refer to Bio::Phylo::Taxa::to_nexus:
-taxa_args => {}	

OR:

# for backward compatibility:
-phylo => $matrix	

SEE ALSO

Bio::Phylo::IO

The newick unparser is called by the Bio::Phylo::IO object. Look there to learn how to unparse newick strings.

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: Nexus.pm 4198 2007-07-12 16:45:08Z rvosa $

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.