Bio::Tools::Run::PhyloUseryContribuBio::Tools::Run::Phylo::Phylip::ProtDist(3)NAMEBio::Tools::Run::Phylo::Phylip::ProtDist - Wrapper for the phylip
program protdist
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 protdist, you will need to modify the protdist source
# code
@params = ('MODEL' => 'PAM');
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my ($matrix) = $protdist_factory->run($aln); # an array of Bio::Matrix::PhylipDist matrix
#finding the distance between two sequences
my $distance = $matrix->get_entry('protein_name_1','protein_name_2');
my @column = $matrix->get_column('protein_name_1');
my @row = $martrix->get_row('protein_name_1');
my @diag = $matrix->get_diagonal();
print $matrix->print_matrix;
#Alternatively, one can create the matrix by passing in a file
#name containing a multiple alignment in phylip format
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my ($matrix) = $protdist_factory->run('/home/shawnh/prot.phy');
# To prevent PHYLIP from truncating sequence names:
# Step 1. Shelf the original names:
my ($aln_safe, $ref_name)= # $aln_safe has serial names
$aln->set_displayname_safe(); # $ref_name holds original names
# Step 2. Run ProtDist and Neighbor:
($matrix) = $protdist_factory->
create_distance_matrix($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;
}
DESCRIPTION
Wrapper for protdist Joseph Felsentein for creating a distance matrix
comparing protein sequences from a multiple alignment file or a
Bio::SimpleAlign object and returns a Bio::Matrix::PhylipDist object;
VERSION Support
This wrapper currently supports v3.5 of phylip. There is also support
for v3.6.
PARAMETERS FOR PROTDIST COMPUTATION
MODEL
Title : MODEL Description : (optional)
This sets the model of amino acid substitution used
in the calculation of the distances. 3 different
models are supported:
PAM Dayhoff PAM Matrix(default)
KIMURA Kimura's Distance CAT
Categories Distance Usage: @params =
('model'=>'X');#where X is one of the values above
Defaults to PAM For more information on the usage of
the different models, please refer to the
documentation
defaults to Equal
(0.25,0.25,0.25,0.25) found in the phylip package.
Additional models in PHYLIP 3.6
PMB - Henikoff/Tillier PMB matrix
JTT - Jones/Taylor/Thornton
MULTIPLE
Title : MULTIPLE Description: (optional)
This allows multiple distance matrices to be generated from multiple
MSA.
Usage: @params = ('MULTIPLE'=>100) where the value specifyies the
number of aligments given.
ALL SUBSEQUENT PARAMETERS WILL ONLY WORK IN CONJUNCTION WITH
THE Categories Distance MODEL*
GENCODE
Title : GENCODE
Description : (optional)
This option allows the user to select among various
nuclear and mitochondrial genetic codes.
Acceptable Values:
U Universal
M Mitochondrial
V Vertebrate mitochondrial
F Fly mitochondrial
Y Yeast mitochondrial
Usage : @params = ('gencode'=>'X');
where X is one of the letters above
Defaults to U
CATEGORY
Title : CATEGORY Description : (optional)
This option sets the categorization of amino acids
all have groups: (Glu Gln Asp Asn), (Lys Arg His),
(Phe Tyr Trp) plus:
G George/Hunt/Barker:
(Cys), (Met Val Leu Ileu),
(Gly Ala Ser Thr Pro)
C Chemical:
(Cys Met), (Val Leu Ileu Gly Ala Ser Thr),
(Pro)
H Hall:
(Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr),
(Pro)
Usage : @params = ('category'=>'X');
where X is one of the letters above
Defaults to G
PROBCHANGE
Title : PROBCHANGE
Description : (optional)
This option sets the ease of changing category of amino
acid. (1.0 if no difficulty of changing,less if less
easy. Can't be negative)
Usage : @params = ('probchange'=>X) where 0<=X<=1
Defaults to 0.4570
TRANS
Title : TRANS
Description : (optional)
This option sets transition/transversion ratio can be
any positive number
Usage : @params = ('trans'=>X) where X >= 0
Defaults to 2
FREQ
Title : FREQ
Description : (optional)
This option sets the frequency of each base (A,C,G,T)
The sum of the frequency must sum to 1.
For example A,C,G,T = (0.25,0.5,0.125,0.125)
Usage : @params = ('freq'=>('W','X','Y','Z')
where W + X + Y + Z = 1
Defaults to Equal (0.25,0.25,0.25,0.25)
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://bugzilla.open-bio.org/
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 : >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';
$matrix= $prodistfactory->run($inputfilename);
or
$seq_array_ref = \@seq_array; @seq_array is array of Seq objs
$aln = $protdistfactory->align($seq_array_ref);
$matrix = $protdistfactory->run($aln);
Function: Create a distance matrix from a SimpleAlign object or a multiple alignment file
Example :
Returns : L<Bio::Matrix::PhylipDist>
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 protdist 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 protdist
create_distance_matrix
Title : create_distance_matrix
Usage : my $file = $app->create_distance_matrix($treefile);
Function: This method is deprecated. Please use run method.
Returns : L<Bio::Matrix::PhylipDist>
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.
_setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for protdist 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 protdist program
Example :
Returns : parameter string to be passed to protdist
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 = $protdist->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 ProtDist 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
perl v5.14.12Bio::Tools::Run::Phylo::Phylip::ProtDist(3)
