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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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