Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       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


         #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,

         my $neighbor_factory =

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


         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 $neighbor_factory =
         my ($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;


         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.

         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

         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

         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

         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

         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


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       participation is much appreciated.
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       Please direct usage questions or support issues to the mailing list:

       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.

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AUTHOR - Shawn Hoon




       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

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

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

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

        Title   : run
        Usage   :
               $inputfilename = 't/data/prot.dist';
               $tree = $neighborfactory->run($inputfilename);
               $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.

        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
                  filename of a tree in newick format

        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

        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

        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

        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

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

        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                                2017-01-Bio::Tools::Run::Phylo::Phylip::Neighbor(3pm)