Provided by: libbio-perl-run-perl_1.7.3-9_all bug

NAME

       Bio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip program protdist

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 protdist, you will need to modify the protdist source
         # code

         @params = ('MODEL' => 'PAM');
         $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);

         my ($matrix)  = $protdist_factory->run($aln); # an array of Bio::Matrix::PhylipDist matrix

         #finding the distance between two sequences
         my $distance = $matrix->get_entry('protein_name_1','protein_name_2');
         my @column   = $matrix->get_column('protein_name_1');
         my @row      = $martrix->get_row('protein_name_1');
         my @diag     = $matrix->get_diagonal();
         print $matrix->print_matrix;

         #Alternatively, one can create the matrix by passing in a file
         #name containing a multiple alignment in phylip format
         $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
         my ($matrix)  = $protdist_factory->run('/home/shawnh/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();      #   $ref_name holds original names
         # Step 2. Run ProtDist and Neighbor:
           ($matrix) = $protdist_factory->
                      create_distance_matrix($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;
           }

DESCRIPTION

       Wrapper for protdist Joseph Felsentein for creating a distance matrix comparing protein
       sequences from a multiple alignment file or a Bio::SimpleAlign object and returns a
       Bio::Matrix::PhylipDist object;

       VERSION Support

       This wrapper currently supports v3.5 of phylip. There is also support for v3.6.

PARAMETERS FOR PROTDIST COMPUTATION

   MODEL
       Title          : MODEL Description    : (optional)

                         This sets the model of amino acid substitution used
                         in the calculation of the distances.  3 different
                         models are supported:
                         PAM     Dayhoff PAM Matrix(default)
                         KIMURA  Kimura's Distance CAT

                         Categories Distance Usage: @params =
                         ('model'=>'X');#where X is one of the values above

                         Defaults to PAM For more information on the usage of
                         the different models, please refer to the
                         documentation
                         defaults to Equal
                         (0.25,0.25,0.25,0.25) found in the phylip package.

                         Additional models in PHYLIP 3.6
                         PMB - Henikoff/Tillier PMB matrix
                         JTT - Jones/Taylor/Thornton

   MULTIPLE
       Title    : MULTIPLE Description: (optional)

                 This allows multiple distance matrices to be generated from multiple
                 MSA.

                 Usage: @params = ('MULTIPLE'=>100) where the value specifyies the
                 number of aligments given.

   ALL SUBSEQUENT PARAMETERS WILL ONLY WORK IN CONJUNCTION WITH
       THE Categories Distance MODEL*

   GENCODE
         Title         : GENCODE
         Description   : (optional)

                         This option allows the user to select among various
                         nuclear and mitochondrial genetic codes.

                         Acceptable Values:
                         U           Universal
                         M           Mitochondrial
                         V           Vertebrate mitochondrial
                         F           Fly mitochondrial
                         Y           Yeast mitochondrial
         Usage         : @params = ('gencode'=>'X');
                         where X is one of the letters above
                         Defaults to U

   CATEGORY
       Title          : CATEGORY Description     : (optional)

                         This option sets the categorization of amino acids
                         all have groups: (Glu Gln Asp Asn), (Lys Arg His),
                         (Phe Tyr Trp)  plus:
                         G   George/Hunt/Barker:
                                 (Cys), (Met   Val  Leu  Ileu),
                                 (Gly  Ala  Ser  Thr  Pro)
                         C   Chemical:
                                 (Cys   Met), (Val  Leu  Ileu  Gly  Ala  Ser  Thr),
                                 (Pro)
                         H   Hall:
                               (Cys), (Met   Val  Leu  Ileu), (Gly  Ala  Ser  Thr),
                               (Pro)

         Usage         : @params = ('category'=>'X');
                         where X is one of the letters above
                         Defaults to G

   PROBCHANGE
         Title       : PROBCHANGE
         Description : (optional)
                        This option sets the ease of changing category of amino
                        acid.  (1.0 if no difficulty of changing,less if less
                        easy. Can't be negative)

         Usage       : @params = ('probchange'=>X) where 0<=X<=1
                       Defaults to 0.4570

   TRANS
         Title       : TRANS
         Description : (optional)
                       This option sets transition/transversion ratio can be
                       any positive number

         Usage        : @params = ('trans'=>X) where X >= 0
                        Defaults to 2

   FREQ
         Title       : FREQ
         Description : (optional)
                       This option sets the frequency of each base (A,C,G,T)
                       The sum of the frequency must sum to 1.
                       For example A,C,G,T = (0.25,0.5,0.125,0.125)

         Usage       : @params = ('freq'=>('W','X','Y','Z')
                       where W + X + Y + Z = 1
                       Defaults to Equal (0.25,0.25,0.25,0.25)

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

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';
               $matrix= $prodistfactory->run($inputfilename);
       or
               $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
               $aln = $protdistfactory->align($seq_array_ref);
               $matrix = $protdistfactory->run($aln);

        Function: Create a distance matrix from a SimpleAlign object or a multiple alignment file
        Example :
        Returns : L<Bio::Matrix::PhylipDist>
        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 protdist 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 protdist

   create_distance_matrix
        Title   : create_distance_matrix
        Usage   : my $file = $app->create_distance_matrix($treefile);
        Function: This method is deprecated. Please use run method.
        Returns : L<Bio::Matrix::PhylipDist>
        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.

   _setinput()
        Title   :  _setinput
        Usage   :  Internal function, not to be called directly
        Function:   Create input file for protdist 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 protdist program
        Example :
        Returns : parameter string to be passed to protdist
        Args    : name of calling object

Bio::Tools::Run::Wrapper methods

   no_param_checks
        Title   : no_param_checks
        Usage   : $obj->no_param_checks($newval)
        Function: Boolean flag as to whether or not we should
                  trust the sanity checks for parameter values
        Returns : value of no_param_checks
        Args    : newvalue (optional)

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

   outfile_name
        Title   : outfile_name
        Usage   : my $outfile = $protdist->outfile_name();
        Function: Get/Set the name of the output file for this run
                  (if you wanted to do something special)
        Returns : string
        Args    : [optional] string to set value to

   tempdir
        Title   : tempdir
        Usage   : my $tmpdir = $self->tempdir();
        Function: Retrieve a temporary directory name (which is created)
        Returns : string which is the name of the temporary directory
        Args    : none

   cleanup
        Title   : cleanup
        Usage   : $codeml->cleanup();
        Function: Will cleanup the tempdir directory after a ProtDist run
        Returns : none
        Args    : none

   io
        Title   : io
        Usage   : $obj->io($newval)
        Function:  Gets a L<Bio::Root::IO> object
        Returns : L<Bio::Root::IO>
        Args    : none

perl v5.36.0                                2023-01-Bio::Tools::Run::Phylo::Phylip::ProtDist(3pm)