Bio::Tools::Run::Phylo::Semphy(3pm)			User Contributed Perl Documentation		       Bio::Tools::Run::Phylo::Semphy(3pm)

NAME

       Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy

SYNOPSIS

	 use Bio::Tools::Run::Phylo::Semphy;

	 # Make a Semphy factory
	 $factory = Bio::Tools::Run::Phylo::Semphy->new();

	 # Run Semphy with an alignment
	 my $tree = $factory->run($alignfilename);

	 # or with alignment object
	 $tree = $factory->run($bio_simplalign);

	 # you can supply an initial tree as well, which can be a newick tree file,
	 # Bio::Tree::Tree object...
	 $tree = $factory->run($bio_simplalign, $tree_obj);

	 # ... or Bio::DB::Taxonomy object
	 $tree = $factory->run($bio_simplalign, $bio_db_taxonomy);

	 # (mixtures of all the above are possible)

	 # $tree isa Bio::Tree::Tree

DESCRIPTION

       This is a wrapper for running the Semphy application by N. Friedman et a.. You can get details here: http://compbio.cs.huji.ac.il/semphy/.
       Semphy is used for phylogenetic reconstruction (making a tree with branch lengths from an aligned set of input sequences).

       You can try supplying normal Semphy command-line arguments to new(), eg.  new(-hky => 1) or calling arg-named methods (excluding the
       initial hyphen(s), eg. $factory->hky(1) to set the --hky switch to true).  Note that Semphy args are case-sensitive. To distinguish between
       Bioperl's -verbose and the Semphy's --verbose, you must set Semphy's verbosity with -semphy_verbose or the semphy_verbose() method.

       You will need to enable this Semphy wrapper to find the Semphy program.	This can be done in (at least) three ways:

	1. Make sure the Semphy executable is in your path.
	2. Define an environmental variable SEMPHYDIR which is a
	   directory which contains the Semphy application:
	   In bash:

	   export SEMPHYDIR=/home/username/semphy/

	   In csh/tcsh:

	   setenv SEMPHYDIR /home/username/semphy

	3. Include a definition of an environmental variable SEMPHYDIR in
	   every script that will use this Semphy wrapper module, e.g.:

	   BEGIN { $ENV{SEMPHYDIR} = '/home/username/semphy/' }
	   use Bio::Tools::Run::Phylo::Semphy;

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:

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

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX

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

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns : string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns : string
	Args	: None

   new
	Title	: new
	Usage	: $factory = Bio::Tools::Run::Phylo::Semphy->new()
	Function: creates a new Semphy factory
	Returns : Bio::Tools::Run::Phylo::Semphy
	Args	: Most options understood by Semphy can be supplied as key =>
		  value pairs, with a true value for switches.

		  These options can NOT be used with this wrapper (they are handled
		  internally or don't make sense in this context):
		  -h | --help | --fill-help
		  -s | --sequence
		  -t | --tree

		  To distinguish between Bioperl's -verbose and the Semphy's --verbose,
		  you must set Semphy's verbosity with -semphy_verbose

   run
	Title	: run
	Usage	: $result = $factory->run($fasta_align_file);
		  -or-
		  $result = $factory->run($align_object);
		  -or-
		  $result = $factory->run($fasta_align_file, $newick_tree_file);
		  -or-
		  $result = $factory->run($align_object, $tree_object);
		  -or-
		  $result = $factory->run($align_object, $db_taxonomy_object);
	Function: Runs Semphy on an alignment.
	Returns : Bio::Tree::Tree
	Args	: The first argument represents an alignment, the second (optional)
		  argument a species tree (to set an initial tree: normally the -t
		  option to Semphy).
		  The alignment can be provided as a multi-fasta format alignment
		  filename, or a Bio::Align::AlignI compliant object (eg. a
		  Bio::SimpleAlign).
		  The species tree can be provided as a newick format tree filename
		  or a Bio::Tree::TreeI compliant object. Alternatively a
		  Bio::DB::Taxonomy object can be supplied, in which case the species
		  tree will be generated by using the alignment sequence names as
		  species names and looking for those in the supplied database.

		  In all cases where an initial tree was supplied, the alignment
		  sequence names must correspond to node ids in the species tree.

   _setparams
	Title	: _setparams
	Usage	: Internal function, not to be called directly
	Function: Creates a string of params to be used in the command string
	Returns : string of params
	Args	: alignment and tree file names

perl v5.12.3							    2011-06-18				       Bio::Tools::Run::Phylo::Semphy(3pm)