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Bio::Tools::Run::PhyloUseryContributed:Perls::Run::Phylo::Phylip::ProtPars(3)

NAME
       Bio::Tools::Run::Phylo::Phylip::ProtPars	- Object for creating a
       Bio::Tree object	from a multiple	alignment file or a SimpleAlign	object

       14 Nov 2002 Shawn Works with Phylip version 3.6

SYNOPSIS
	 #Create a SimpleAlign object
	 @params = ('ktuple' =>	2, 'matrix' => 'BLOSUM');
	 $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
	 $inputfilename	= 't/data/cysprot.fa';
	 $aln =	$factory->run($inputfilename); # $aln is a SimpleAlign object.

	 #Create the Tree
	 #using	a threshold value of 30	and id name lengths limit of 30
	 #note to use id name length greater than the standard 10 in protpars,
	 # you will need to modify the protpars	source code
	 $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->
	    new(idlength=>30,threshold=>10,jumble=>"17,10",outgroup=>2);
	 $tree = $tree_factory->run($aln);

	 #Or one can pass in a file name containing a multiple alignment
	 #in phylip format:

	 $tree_factory =
	   Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10);
	 $tree = $tree_factory->run("/usr/users/shawnh/COMPARA/prot.phy");

	 # To prevent PHYLIP from truncating sequence names:
	 # Step	1. Shelf the original names:
	    my ($aln_safe, $ref_name)=			  #   $aln_safe	has serial names
		       $aln->set_displayname_safe();	  #   $ref_name	holds original names
	 # Step	2. Run ProtPars:
	    $tree = $protpars_factory->run($aln_safe);	  #  Use $aln_safe instead of $aln
	 # Step	3. Retrieve orgininal OTU names:
	    use	Bio::Tree::Tree;
	    my @nodes=$tree->get_nodes();
		foreach	my $nd (@nodes){
		   $nd->id($ref_name->{$nd->id_output})	if $nd->is_Leaf;
		}

PARAMTERS FOR PROTPARS COMPUTATION
   THRESHOLD
       Title	      :	THRESHOLD Description	 : (optional)
			 This sets a threshold such that if the	number of
			 steps counted in a character is higher	than the
			 threshold, it will be taken to	be the threshold
			 value rather than the actual number of	steps.	You
			 should	use a positive real number greater than	1.
			 Please	see the	documetation from the phylip package
			 for more information.

   OUTGROUP
       Title	      :	OUTGROUP Description	: (optional)

			 This specifies	which species is to be used to root
			 the tree by having it become the outgroup.  Input
			 values	are integers specifying	which species to use.
			 Defaults to 1

   JUMBLE
       Title	      :	JUMBLE Description     : (optional)
			 This enables you to tell the program to use a random
			 number	generator to choose the	input order of
			 species.  Input values	is of the format:
			 seed,iterations eg 17,10 seed:	an integer between 1
			 and 32767 and of the form 4n+1	which means that it
			 must give a remainder of 1 when divided by 4.	Each
			 different seed	leads to a different sequence of
			 addition of species.  By simply changing the random
			 number	seed and re-running programs one can look for
			 other,	and better trees.  iterations: For a value of
			 10, this will tell the	program	to try ten different
			 orders	of species in constructing the trees, and the
			 results printed out will reflect this entire search
			 process (that is, the best trees found	among all 10
			 runs will be printed out, not the best	trees from
			 each individual run).

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 one
       of the Bioperl mailing lists.  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
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

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

AUTHOR - Shawn Hoon
       Email shawnh@fugu-sg.org

CONTRIBUTORS
       Email jason-AT-bioperl_DOT_org

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	: >program_name()
	Function: holds	the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: ->program_dir()
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   idlength
	Title	: idlength
	Usage	: $obj->idlength ($newval)
	Function:
	Returns	: value	of idlength
	Args	: newvalue (optional)

   run
	Title	: run
	Usage	:
	       $inputfilename =	't/data/prot.phy';
	       $tree = $factory->run($inputfilename);
       or
	       $seq_array_ref =	\@seq_array; @seq_array	is array of Seq	objs
	       $aln = $factory->run($seq_array_ref);
	       $tree = $treefactory->run($aln);
	Function: Create a protpars tree from a	SimpleAlign object
	Example	:
	Returns	: L<Bio::Tree> object
	Args	: Name of a file containing a multiple alignment in Phylip format
		  or an	SimpleAlign object

	Throws an exception if argument	is not either a	string (eg a
	filename) or a Bio::SimpleAlign	object.	If
	argument is string, throws exception if	file corresponding to string
	name can not be	found.

   create_tree
	Title	: create_tree
	Usage	:
	 $inputfilename	= 't/data/prot.phy';
	 $tree = $factory->create_tree($inputfilename);
       or
	 $seq_array_ref	= \@seq_array; @seq_array is array of Seq objs
	 $aln =	$factory->align($seq_array_ref);
	 $tree = $treefactory->create_tree($aln);
	Function: Create a protpars tree from a	SimpleAlign object
	Example	:
	Returns	: L<Bio::Tree> object
	Args	: Name of a file containing a multiple alignment in Phylip format
		  or an	SimpleAlign object

	Throws an exception if argument	is not either a	string (eg a
	filename) or a Bio::SimpleAlign	object.	If
	argument is string, throws exception if	file corresponding to string
	name can not be	found.

   _run
	Title	:  _run
	Usage	:  Internal function, not to be	called directly
	Function:   makes actual system	call to	protpars program
	Example	:
	Returns	: Bio::Tree object
	Args	: Name of a file containing a set of multiple alignments
		  in Phylip format and a parameter string to be	passed to protpars

   _setinput()
	Title	:  _setinput
	Usage	:  Internal function, not to be	called directly
	Function:   Create input file for protpars program
	Example	:
	Returns	: name of file containing a multiple alignment in Phylip format
	Args	: SimpleAlign object reference or input	file name

   _setparams()
	Title	:  _setparams
	Usage	:  Internal function, not to be	called directly
	Function:   Create parameter inputs for	protpars program
	Example	:
	Returns	: parameter string to be passed	to protpars
	Args	: name of calling object

perl v5.32.1			  2Bio::Tools::Run::Phylo::Phylip::ProtPars(3)

NAME | SYNOPSIS | PARAMTERS FOR PROTPARS COMPUTATION | FEEDBACK | AUTHOR - Shawn Hoon | CONTRIBUTORS | APPENDIX

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