Provided by: libbio-perl-run-perl_1.6.9-1_all bug

NAME

       Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a Bio::Tree object from a
       multiple alignment file or a SimpleAlign object

       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 Tree
         #using a threshold value of 30 and id name lengths limit of 30
         #note to use id name length greater than the standard 10 in protpars,
         # you will need to modify the protpars source code
         $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->
            new(idlength=>30,threshold=>10,jumble=>"17,10",outgroup=>2);
         $tree = $tree_factory->run($aln);

         #Or one can pass in a file name containing a multiple alignment
         #in phylip format:

         $tree_factory =
           Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10);
         $tree = $tree_factory->run("/usr/users/shawnh/COMPARA/prot.phy");

         # 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 ProtPars:
            $tree = $protpars_factory->run($aln_safe);    #  Use $aln_safe instead of $aln
         # Step 3. Retrieve orgininal OTU names:
            use Bio::Tree::Tree;
            my @nodes=$tree->get_nodes();
                foreach my $nd (@nodes){
                   $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
                }

PARAMTERS FOR PROTPARS COMPUTATION

   THRESHOLD
       Title          : THRESHOLD Description    : (optional)
                         This sets a threshold such that if the number of
                         steps counted in a character is higher than the
                         threshold, it will be taken to be the threshold
                         value rather than the actual number of steps.  You
                         should use a positive real number greater than 1.
                         Please see the documetation from the phylip package
                         for more information.

   OUTGROUP
       Title          : OUTGROUP Description    : (optional)

                         This specifies which species is to be used to root
                         the tree by having it become the outgroup.  Input
                         values are integers specifying which species to use.
                         Defaults to 1

   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.  Input values is of the format:
                         seed,iterations eg 17,10 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: For a value of
                         10, this will tell the program to try ten different
                         orders of species in constructing the trees, and the
                         results printed out will reflect this entire search
                         process (that is, the best trees found among all 10
                         runs will be printed out, not the best trees from
                         each individual run).

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_DOT_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.phy';
               $tree = $factory->run($inputfilename);
       or
               $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
               $aln = $factory->run($seq_array_ref);
               $tree = $treefactory->run($aln);
        Function: Create a protpars tree from a SimpleAlign object
        Example :
        Returns : L<Bio::Tree> object
        Args    : Name of a file containing a multiple alignment in Phylip format
                  or an SimpleAlign object

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

   create_tree
        Title   : create_tree
        Usage   :
         $inputfilename = 't/data/prot.phy';
         $tree = $factory->create_tree($inputfilename);
       or
         $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
         $aln = $factory->align($seq_array_ref);
         $tree = $treefactory->create_tree($aln);
        Function: Create a protpars tree from a SimpleAlign object
        Example :
        Returns : L<Bio::Tree> object
        Args    : Name of a file containing a multiple alignment in Phylip format
                  or an SimpleAlign object

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

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

   _setinput()
        Title   :  _setinput
        Usage   :  Internal function, not to be called directly
        Function:   Create input file for protpars program
        Example :
        Returns : name of file containing a multiple alignment in Phylip format
        Args    : SimpleAlign object reference or input file name

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

perl v5.12.3                                2011-06-Bio::Tools::Run::Phylo::Phylip::ProtPars(3pm)