Provided by: libbio-perl-run-perl_1.7.1-3_all 
NAME
Bio::Tools::Run::Phylo::Phylip::ProtPars - Object for creating a Bio::Tree object from a
multiple alignment file or a SimpleAlign object
14 Nov 2002 Shawn Works with Phylip version 3.6
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.
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
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
perl v5.24.1 2017-01-Bio::Tools::Run::Phylo::Phylip::ProtPars(3pm)