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

NAME
       Bio::Tools::Run::Phylo::Phylip::Neighbor	- Wrapper for the phylip
       program neighbor	by Joseph Felsenstein for creating a phylogenetic
       tree(either through Neighbor or UPGMA) based on protein distances based
       on amino	substitution rate.

       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 Distance Matrix
	 # using a default PAM matrix and id name lengths limit	of 30 note to
	 # use id name length greater than the standard	10 in neighbor,	you
	 # will	need to	modify the neighbor source code

	 $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
	 my $matrix  = $protdist_factory->run($aln);

	 #Create the tree passing in the distance matrix
	 @params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
		    'upptri'=>1,'subrep'=>1);

	 my $neighbor_factory =
	    Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);

	 #you can set your outgroup using either a number specifying
	 #the rank in the matrix or you	can just use the name of the
	 #species

	 $neighbor_factory->outgroup('ENSP00001');
	 #or
	 $neighbor_factory->outgroup(1);

	 my ($tree) = $neighbor_factory->run($matrix);

	 # Alternatively, one can create the tree by passing in	a file name
	 # containing a	phylip formatted distance matrix(using protdist)
	 my $neighbor_factory =
	   Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
	 my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist');

	 # 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 ProtDist	and Neighbor:
	   $matrix  = $protdist_factory->
		       creat_distance_matrix($aln_safe); #  Use	$aln_safe instead of $aln
	   $tree = $neighbor_factory->run($matrix);
	 # 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 NEIGHBOR COMPUTATION
   TYPE
	 Title	       : TYPE
	 Description   : (optional)
			 This sets the type of tree to construct, using
			 neighbor joining or UPGMA.

			 NJ    Neighbor	Joining
			 UPGMA UPGMA

	 Usage	       : @params = ('type'=>'X');#where	X is one of the	values above
			 Defaults to NJ

			 For more information on the usage of the different
			 models, please	refer to the documentation found in
			 the phylip package.

   OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)
	 Title	       : OUTGROUP
	 Description   : (optional)
			 This option selects the species to be used as the outgroup
	 Acceptable Values: integer
	 Usage	       : @params = ('outgroup'=>'X');
			 where X is an positive	integer	not more than the
			 number	of sequences
			 Defaults to 1

   LOWTRI
	 Title	       : LOWTRI
	 Description   : (optional)
			 This indicates	that the distance matrix is
			 input	in  Lower-triangular form  (the	 lower-left
			 half of the distance matrix only, without the zero
			 diagonal elements)
	 Usage	       : @params = ('lowtri'=>'X'); where X is either 1	or 0
			 Defaults to 0

   UPPTRI
	 Title	       : UPPTRI
	 Description   : (optional)
			 This indicates	that the distance matrix is input  in
			 upper-triangular form	(the  upper-right half of the
			 distance matrix only, without the zero	diagonal elements.)
       Usage	       : @params = ('upptri'=>'X'); where X is either 1	or 0
			 Defaults to 0

   SUBREP
	 Title	       : SUBREP
	 Description   : (optional)
			 This is the Subreplication option.

			 It informs the	program	that after each	distance will
			 be provided an	integer	indicating that	the distance
			 is a mean of that many	replicates.

	 Usage	       : @params = ('subrep'=>'X'); where X is either 1	or 0
			 Defaults to 0

   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.  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:

	 Usage	      :	@params	= ('jumble'=>'17); where 17 is the random seed
			Defaults to no jumble

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.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.dist';
	       $tree = $neighborfactory->run($inputfilename);
	or
	       $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
	       $matrix	= $protdist_factory->create_distance_matrix($aln);
	       $tree= $neighborfactory->run($matrix);

	Function: a Bio:Tree from a protein distance matrix created by protidst
	Example	:
	Returns	: Bio::Tree
	Args	: Name of a file containing a protein distance matrix in Phylip	format
		  or a hash ref	to a matrix

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

   create_tree
	Title	: create_tree
	Usage	: my $file = $app->create_tree($treefile);
	Function: This method is deprecated. Please use	run method.
	Returns	: File containing the rendered tree
	Args	: either a Bio::Tree::TreeI
		   OR
		  filename of a	tree in	newick format

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

   _setinput()
	Title	: _setinput
	Usage	: Internal function, not to be called directly
	Function: Create input file for	neighbor program
	Example	:
	Returns	: name of file containing the protein distance matrix in Phylip	format
	Args	: name of file created by protdist or ref to hash created by
		  Bio::Tools:Run::Phylo::Phylip::ProtDist

   names()
	Title	:  names
	Usage	:  $tree->names(\%names)
	Function:  get/set for a hash ref for storing names in matrix
		   with	rank as	values.
	Example	:
	Returns	: hash reference
	Args	: hash reference

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

   outfile
	Title	: outfile
	Usage	: $obj->outfile($newval)
	Function: Get/Set default PHYLIP outfile name ('outfile' usually)
	Returns	: value	of outfile
	Args	: newvalue (optional)

   treefile
	Title	: treefile
	Usage	: $obj->treefile($newval)
	Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
	Returns	: value	of treefile
	Args	: newvalue (optional)

perl v5.24.1			  2Bio::Tools::Run::Phylo::Phylip::Neighbor(3)

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

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