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)