/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phylo::Phylip::Neighbor

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');

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

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://bugzilla.open-bio.org/

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, obtiained 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)