.\" -*- mode: troff; coding: utf-8 -*-
.\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>.
.ie n \{\
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Phylo::Phylip::ProtPars 3pm"
.TH Bio::Tools::Run::Phylo::Phylip::ProtPars 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH NAME
Bio::Tools::Run::Phylo::Phylip::ProtPars \- Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object
.PP
14 Nov 2002 Shawn
Works with Phylip version 3.6
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 5
\&  #Create a SimpleAlign object
\&  @params = (\*(Aqktuple\*(Aq => 2, \*(Aqmatrix\*(Aq => \*(AqBLOSUM\*(Aq);
\&  $factory = Bio::Tools::Run::Alignment::Clustalw\->new(@params);
\&  $inputfilename = \*(Aqt/data/cysprot.fa\*(Aq;
\&  $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;
\&         }
.Ve
.SH "PARAMTERS FOR PROTPARS COMPUTATION"
.IX Header "PARAMTERS FOR PROTPARS COMPUTATION"
.SS THRESHOLD
.IX Subsection "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.
.SS OUTGROUP
.IX Subsection "OUTGROUP"
Title		: OUTGROUP
Description	: (optional)
.PP
.Vb 4
\&                  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
.Ve
.SS JUMBLE
.IX Subsection "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).
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email shawnh@fugu\-sg.org
.SH CONTRIBUTORS
.IX Header "CONTRIBUTORS"
Email jason\-AT\-bioperl_DOT_org
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : >program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : \->program_dir()
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS idlength
.IX Subsection "idlength"
.Vb 5
\& Title   : idlength 
\& Usage   : $obj\->idlength ($newval)
\& Function: 
\& Returns : value of idlength 
\& Args    : newvalue (optional)
.Ve
.SS run
.IX Subsection "run"
.Vb 10
\& Title   : run 
\& Usage   :
\&        $inputfilename = \*(Aqt/data/prot.phy\*(Aq;
\&        $tree = $factory\->run($inputfilename);
\&or
\&        $seq_array_ref = \e@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.
.Ve
.SS create_tree
.IX Subsection "create_tree"
.Vb 10
\& Title   : create_tree 
\& Usage   :
\&  $inputfilename = \*(Aqt/data/prot.phy\*(Aq;
\&  $tree = $factory\->create_tree($inputfilename);
\&or
\&  $seq_array_ref = \e@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.
.Ve
.SS _run
.IX Subsection "_run"
.Vb 7
\& 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
.Ve
.SS \fB_setinput()\fP
.IX Subsection "_setinput()"
.Vb 6
\& 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
.Ve
.SS \fB_setparams()\fP
.IX Subsection "_setparams()"
.Vb 6
\& 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
.Ve