/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Phylip::Consense

NAME

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

SYNOPSIS

use Bio::Tools::Run::Phylo::Phylip::Consense;
use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
use Bio::Tools::Run::Phylo::Phylip::ProtDist;
use Bio::Tools::Run::Phylo::Phylip::Neighbor;
use Bio::Tools::Run::Phylo::Phylip::DrawTree;


#first get an alignment
my $aio= Bio::AlignIO->new(-file=>$ARGV[0],-format=>"clustalw");
my $aln = $aio->next_aln;

# To prevent truncation of sequence names by PHYLIP runs, use set_displayname_safe
my ($aln_safe, $ref_name)=$aln->set_displayname_safe();

#next use seqboot to generate multiple aligments
my @params = ('datatype'=>'SEQUENCE','replicates'=>10);
my $seqboot_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);

my $aln_ref= $seqboot_factory->run($aln);

Or, for long sequence names:

my $aln_ref= $seqboot_factory->run($aln_safe);

#next build distance matrices and construct trees
my $pd_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
my $ne_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();

foreach my $a (@{$aln_ref}){
  my $mat = $pd_factory->create_distance_matrix($a);
  push @tree, $ne_factory->create_tree($mat);
}

#now use consense to get a final tree
my $con_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();

#you may set outgroup either by the number representing the order in
#which species are entered or by the name of the species

$con_factory->outgroup(1);
$con_factory->outgroup('HUMAN');

my $tree = $con_factory->run(\@tree);

# Restore original sequence names, after ALL phylip runs:
my @nodes = $tree->get_nodes();
foreach my $nd (@nodes){
   $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
}

#now draw the tree
my $draw_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
my $image_filename = $draw_factory->draw_tree($tree);

DESCRIPTION

Wrapper for phylip consense program

Taken from phylip documentation...

CONSENSE reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree. At the moment it carries out a family of consensus tree methods called the M[l] methods (Margush and McMorris, 1981). These include strict consensus and majority rule consensus. Basically the consensus tree consists of monophyletic groups that occur as often as possible in the data.

More documentation on using Consense and setting parameters may be found in the phylip package.

VERSION Support

This wrapper currently supports v3.5 of phylip. There is also support for v3.6 although this is still experimental as v3.6 is still under alpha release and not all functionalities maybe supported.

PARAMETERS FOR Consense

TYPE

Title : TYPE Description : (optional) Only available in phylip v3.6

     This program supports 3 types of consensus generation 

     MRe   : Majority Rule (extended) Any set of species that
             appears in more than 50% of the trees is included. 
             The program then considers the other sets of species 
             in order of the frequency with which they have appeared, 
             adding to the consensus tree any which are compatible 
             with it until

     STRICT: A set of species must appear in all input trees to be 
             included in the strict consensus tree. 

     MR    :  A set of species is included in the consensus tree 
             if it is present in more than half of the input trees. 

     Ml    : The user is asked for a fraction between 0.5 and 1, and 
             the program then includes in the consensus tree any set 
             of species that occurs among the input trees more than 
             that fraction of then time. The Strict consensus and the 
             Majority Rule consensus are extreme cases of the M[l] consensus,
             being for fractions of 1 and 0.5 respectively

     usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-type=>"Ml 0.7");


Defaults to MRe

ROOTED

Title: ROOTED 
Description: (optional)

           toggles between the default assumption that the input trees are unrooted trees and 
           the selection that specifies that the tree is to be treated as a rooted tree and not 
           re-rooted. Otherwise the tree will be treated as outgroup-rooted and will be
           re-rooted automatically at the first species encountered on the first tree 
           (or at a species designated by the Outgroup option)

           usage: my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-rooted=>1);

           Defaults to unrooted

OUTGROUP

Title		: OUTGROUP
Description	: (optional)

              It is in effect only if the Rooted option selection is not in effect.
              The trees will be re-rooted with a species of your choosing.

              usage  my $factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-outgroup=>2);

              Defaults to first species encountered.

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   : $obj->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.treefile';
	$tree= $Consense_factory->run($inputfilename);
or

	$tree= $consense_factory->run(\@tree);

 Function: Create bootstrap sets of alignments
 Example :
 Returns : a L<Bio::Tree::Tree>
 Args    : either a file containing trees in newick format
           or an array ref of L<Bio::Tree::Tree>

 Throws an exception if argument is not either a string (eg a
 filename) or a Bio::Tree::TreeI 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 Consense program
Example :
Returns : an array ref of <Bio::Tree::Tree> 
Args    : Name of a file containing a set of tree in newick format 
          and a parameter string to be passed to Consense

_setinput()

Title   :  _setinput
Usage   :  Internal function, not to be called directly	
Function:   Create input file for Consense program
Example :
Returns : name of file containing a trees in newick format
Args    : an array ref of Bio::Tree::Tree object or input file name

names()

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

_setparams()

Title   :  _setparams
Usage   :  Internal function, not to be called directly	
Function:   Create parameter inputs for Consense program
Example :
Returns : parameter string to be passed to Consense
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 = $Consense->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 Consense 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