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 programTaken 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 : TYPEDescription : (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.
[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: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]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