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 neighbor, you
# will need to modify the neighbor source code
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my $matrix = $protdist_factory->run($aln);
#Create the tree passing in the distance matrix
@params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
'upptri'=>1,'subrep'=>1);
my $neighbor_factory =
Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
#you can set your outgroup using either a number specifying
#the rank in the matrix or you can just use the name of the
#species
$neighbor_factory->outgroup('ENSP00001');
#or
$neighbor_factory->outgroup(1);
my ($tree) = $neighbor_factory->run($matrix);
# Alternatively, one can create the tree by passing in a file name
# containing a phylip formatted distance matrix(using protdist)
my $neighbor_factory =
Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist');
# To prevent PHYLIP from truncating sequence names:
# Step 1. Shelf the original names:
my ($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 = $protdist_factory->
creat_distance_matrix($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;
}
PARAMTERS FOR NEIGHBOR COMPUTATION
TYPE
Title : TYPE
Description : (optional)
This sets the type of tree to construct, using
neighbor joining or UPGMA.
NJ Neighbor Joining
UPGMA UPGMA
Usage : @params = ('type'=>'X');#where X is one of the values above
Defaults to NJ
For more information on the usage of the different
models, please refer to the documentation found in
the phylip package.
OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)
Title : OUTGROUP
Description : (optional)
This option selects the species to be used as the outgroup
Acceptable Values: integer
Usage : @params = ('outgroup'=>'X');
where X is an positive integer not more than the
number of sequences
Defaults to 1
LOWTRI
Title : LOWTRI
Description : (optional)
This indicates that the distance matrix is
input in Lower-triangular form (the lower-left
half of the distance matrix only, without the zero
diagonal elements)
Usage : @params = ('lowtri'=>'X'); where X is either 1 or 0
Defaults to 0
UPPTRI
Title : UPPTRI
Description : (optional)
This indicates that the distance matrix is input in
upper-triangular form (the upper-right half of the
distance matrix only, without the zero diagonal elements.)
Usage : @params = ('upptri'=>'X'); where X is either 1 or 0
Defaults to 0
SUBREP
Title : SUBREP
Description : (optional)
This is the Subreplication option.
It informs the program that after each distance will
be provided an integer indicating that the distance
is a mean of that many replicates.
Usage : @params = ('subrep'=>'X'); where X is either 1 or 0
Defaults to 0
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. 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:
Usage : @params = ('jumble'=>'17); where 17 is the random seed
Defaults to no jumble
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]CONTRIBUTORS
Email:jason-at-bioperl.orgAPPENDIX
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.dist';
$tree = $neighborfactory->run($inputfilename);
or
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
$matrix = $protdist_factory->create_distance_matrix($aln);
$tree= $neighborfactory->run($matrix);
Function: a Bio:Tree from a protein distance matrix created by protidst
Example :
Returns : Bio::Tree
Args : Name of a file containing a protein distance matrix in Phylip format
or a hash ref to a matrix
Throws an exception if argument is not either a string (eg a
filename) or a Hash. If argument is string, throws exception
if file corresponding to string name can not be found.
create_tree
Title : create_tree
Usage : my $file = $app->create_tree($treefile);
Function: This method is deprecated. Please use run method.
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
_run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to neighbor program
Example :
Returns : Bio::Tree object
Args : Name of a file containing protein distances in Phylip format
and a parameter string to be passed to neighbor
_setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for neighbor program
Example :
Returns : name of file containing the protein distance matrix in Phylip format
Args : name of file created by protdist or ref to hash created by
Bio::Tools:Run::Phylo::Phylip::ProtDist
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 neighbor program Example : Returns : parameter string to be passed to neighbor Args : name of calling object
outfile
Title : outfile
Usage : $obj->outfile($newval)
Function: Get/Set default PHYLIP outfile name ('outfile' usually)
Returns : value of outfile
Args : newvalue (optional)
treefile
Title : treefile
Usage : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args : newvalue (optional)