bp_tree2pag(1p) [debian man page]

BP_TREE2PAG(1p) 					User Contributed Perl Documentation					   BP_TREE2PAG(1p)

NAME

       tree2pag - convert Bio::TreeIO parseable format trees to pagel format

SYNOPSIS

	tree2pag -if nexus -i file.nexus > file.pag

	# OR pipe in through STDIN, and use newick format instead

	cat file.newick | tree2pag -if newick > file.nh

	# OR specify an output and input

	tree2pag -o file.pag -i file.newick

DESCRIPTION

       Convert TreeIO parseable files into Pagel format tree files.  Be warned that pagel format only really supports a single tree per file so.
       Also Pagel parsing is not yet available in bioperl.

perl v5.14.2							    2012-03-02							   BP_TREE2PAG(1p)

Bio::TreeIO(3pm)					User Contributed Perl Documentation					  Bio::TreeIO(3pm)

NAME

       Bio::TreeIO - Parser for Tree files

SYNOPSIS

	 {
	     use Bio::TreeIO;
	     my $treeio = Bio::TreeIO->new('-format' => 'newick',
			  '-file'   => 'globin.dnd');
	     while( my $tree = $treeio->next_tree ) {
		       print "Tree is ", $tree->number_nodes, "
";
	     }
	 }

DESCRIPTION

       This is the driver module for Tree reading from data streams and flatfiles.  This is intended to be able to create Bio::Tree::TreeI
       objects.

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 via the
       web:

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

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

CONTRIBUTORS

       Allen Day <allenday@ucla.edu>

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::TreeIO->new();
	Function: Builds a new Bio::TreeIO object
	Returns : Bio::TreeIO
	Args	: a hash.  useful keys:
	  -format : Specify the format of the file.  Supported formats:

	    newick	       Newick tree format
	    nexus	       Nexus tree format
	    nhx 	       NHX tree format
	    svggraph	       SVG graphical representation of tree
	    tabtree	       ASCII text representation of tree
	    lintree	       lintree output format

   next_tree
	Title	: next_tree
	Usage	: my $tree = $treeio->next_tree;
	Function: Gets the next tree off the stream
	Returns : Bio::Tree::TreeI or undef if no more trees
	Args	: none

   write_tree
	Title	: write_tree
	Usage	: $treeio->write_tree($tree);
	Function: Writes a tree onto the stream
	Returns : none
	Args	: Bio::Tree::TreeI

   attach_EventHandler
	Title	: attach_EventHandler
	Usage	: $parser->attatch_EventHandler($handler)
	Function: Adds an event handler to listen for events
	Returns : none
	Args	: Bio::Event::EventHandlerI

   _eventHandler
	Title	: _eventHandler
	Usage	: private
	Function: Get the EventHandler
	Returns : Bio::Event::EventHandlerI
	Args	: none

   _load_format_module
	Title	: _load_format_module
	Usage	: *INTERNAL TreeIO stuff*
	Function: Loads up (like use) a module at run time on demand
	Example :
	Returns :
	Args	:

   _guess_format
	Title	: _guess_format
	Usage	: $obj->_guess_format($filename)
	Function:
	Example :
	Returns : guessed format of filename (lower case)
	Args	:

perl v5.14.2							    2012-03-02							  Bio::TreeIO(3pm)