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Bio::Tools::Run::Phylo::Molphy::ProtML.3pm

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