Bio::Tools::Run::Phylo::Molphy::ProtML man page on Pidora

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Bio::Tools::Run::PhyloUserlContributeBio::Tools::Run::Phylo::Molphy::ProtML(3)

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 = Bio::Tools::Run::Phylo::Molphy::ProtML->new(-verbose => $verbose,
								 -flags	  => \%args);

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

	 # read in a previously built protein alignment
	 my $in = Bio::AlignIO->new(-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 = Bio::TreeIO->new(-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/ismlib/softother.e.html>.	Note
       that PHYLIP (Joe Felsenstein) also provides a version of 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.

	 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/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 of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-AT-bioperl_DOT_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, obtained from ENV variable.
	Returns:  string
	Args	:

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Run::Phylo::Molphy::ProtML->new();
	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

perl v5.14.1			  201Bio::Tools::Run::Phylo::Molphy::ProtML(3)
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