/ 
bioperl-run-1.4
/ Bio::Tools::Run::Phylo::Molphy::ProtML

NAME

Bio::Tools::Run::Phylo::Molphy::ProtML - A wrapper for the Molphy pkg app ProtML

SYNOPSIS

use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Molphy::ProtML;

my %args = ( 'models' => 'jtt',
	     'search' => 'quick',
	     "other" => [ '-information', '-w']);
my $verbose = 0; # change to 1 if you want some debugging output
my $protml = new Bio::Tools::Run::Phylo::Molphy::ProtML(-verbose => $verbose,
							   -flags => \%args);

die("cannot find the protml executable") unless $protml->executable;

# read in a previously built protein alignment
my $in = new Bio::AlignIO(-format => 'clustalw',
			    -file   => 't/data/cel-cbr-fam.aln');
my $aln = $in->next_aln;
$protml->alignment($aln);

my ($rc,$results) = $protml->run();

# This may be a bit of overkill, but it is possible we could
# have a bunch of results and $results is a
# Bio::Tools::Phylo::Molphy object

my $r = $results->next_result;
# $r is a Bio::Tools::Phylo::Molphy::Result object

my @trees;
while( my $t = $r->next_tree ) {
    push @trees, $t;
}

print "search space is ", $r->search_space, "\n";
      "1st tree score is ", $tree[0]->score, "\n";

my $out = new Bio::TreeIO(-file => ">saved_MLtrees.tre",
                          -format => "newick");
$out->write_tree($tree[0]);
$out = undef;

DESCRIPTION

This is a wrapper for the exe from the Molphy (MOLecular PHYlogenetics) package by Jun Adachi & Masami Hasegawa. The software can be downloaded from http://www.ism.ac.jp/software/ismlib/softother.e.html or http://ftp.ism.ac.jp:8000/ISMLIB/MOLPHY/ websites. Note that the PHYLIP (Joe Felsenstein) also provides a version of the protml which this module is currently NOT prepared to handle. Use the package available directly from MOLPHY authors if you want to use the module in its present implementation, (extensions are welcomed!).

The main components are the protml and nucml executables which are used to build maximum likelihood (ML) phylogenetic trees based on either protein or nucleotide sequences.

Here are the valid input parameters, we have added a longhand version of the parameters to help you understand what each one does. Either the longhand or the original Molphy parameter will work.

on the left while the Molphy parameter is on the

Bioperl      Molphy           Description
Longhand     parameter
Model (one of these):
---------------
 jtt             j            Jones, Taylor & Thornton (1992)
jtt-f            jf           JTT w/ frequencies
dayhoff          d            Dahoff et al. (1978)
dayhoff-f        d            dayhoff w/ frequencies
mtrev24          m            mtREV24 Adachi & Hasegwa (1995)
mtrev24-f        mf           mtREV24 w/ frequencies
poisson          p            Poisson
proportional     pf           Proportional
  rsr            r            Relative Substitution Rate
 rsr-f           rf           RSR w/ frequencies
frequencies      f            data frequencies

Search Strategy (one of these):
----------------
usertrees        u            User trees (must also supply a tree)
rearrangement    R            Local rearrangement
    lbp          RX           Local boostrap prob
exhaustive       e            Exhaustive search
   star          s            Star decomposition search (may not be ML)
   quick         q            Quick Add OTU search (may not be ML)
 distance        D            ML Distance matrix --> NJDIST (need to supply
							     NJDIST tree)


Others (can be some or all of these):
---------------
norell-bp        b            No RELL-BP
minimumevolution M            Minimum evolution

sequential       S            Sequence is in Sequential format
                   _OR_
interleaved      I            Sequence is in Interleaved format

verbose          v            Verbose messages directed to STDERR
information      i            Output some information (tree vals)
		 w            More some extra information (transition
							   matricies, etc)

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 the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Additional contributors names and emails here

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, obtiained from ENV variable.
Returns:  string
Args    :

new

 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::Phylo::Molphy::ProtML();
 Function: Builds a new Bio::Tools::Run::Phylo::Molphy::ProtML object
 Returns : Bio::Tools::Run::Phylo::Molphy::ProtML
 Args    : -alignment => the Bio::Align::AlignI object
           -save_tempfiles => boolean to save the generated tempfiles and
                              NOT cleanup after onesself (default FALSE)
           -tree => the Bio::Tree::TreeI object
           -params => a hashref of PAML parameters (all passed to
						    set_parameter)
           -executable => where the protml executable resides

See also: Bio::Tree::TreeI, Bio::Align::AlignI

run

Title   : run
Usage   : $protml->run();
Function: run the protml analysis using the default or updated parameters
          the alignment parameter must have been set
Returns : Bio::Tools::Phylo::Molphy
Args    :

alignment

Title   : alignment
Usage   : $protml->align($aln);
Function: Get/Set the Bio::Align::AlignI object
Returns : Bio::Align::AlignI object
Args    : [optional] Bio::Align::AlignI
Comment : We could potentially add support for running directly on a file
          but we shall keep it simple
See also : L<Bio::SimpleAlign>, L<Bio::Align::AlignI>

tree

Title   : tree
Usage   : $protml->tree($tree, %params);
Function: Get/Set the Bio::Tree::TreeI object
Returns : Bio::Tree::TreeI
Args    : [optional] $tree => Bio::Tree::TreeI,

Comment : We could potentially add support for running directly on a file
          but we shall keep it simple
See also : L<Bio::Tree::Tree>

get_flags

Title   : get_flags
Usage   : my @params = $protml->get_flags();
Function: returns the list of flags
Returns : array of flag names coded in the way that
Args    : none

set_flag

Title   : set_flag
Usage   : $protml->set_parameter($type,$val);
Function: Sets a protml parameter, will be validated against
          the valid values as set in the %VALIDVALUES class variable.
          The checks can be ignored if one turns off param checks like this:
            $protml->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
          then no warning will be reported
Args    : $type => name of the parameter
          This can be one of 'search', 'model', 'other'
          $value => flag value
See also: L<no_param_checks()>

get_parameters

Title   : get_parameters
Usage   : my %params = $protml->get_parameters();
Function: returns the list of parameters as a hash
Returns : associative array keyed on parameter names
Args    : none

set_parameter

Title   : set_parameter
Usage   : $protml->set_parameter($param,$val);
Function: Sets a protml parameter, will be validated against
          the valid values as set in the %VALIDVALUES class variable.
          The checks can be ignored if one turns off param checks like this:
            $protml->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
          then no warning will be reported
Args    : $param => name of the parameter
          $value => value to set the parameter to
See also: L<no_param_checks()>

Bio::Tools::Run::WrapperBase 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 = $protml->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   : $protml->cleanup();
Function: Will cleanup the tempdir directory after a PAML 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