Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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://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, 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)