# Build a Raxml factory
  $factory = Bio::Tools::Run::Phylo::Raxml->new(-p  => 100);

  # Get an alignment
  my $alignio = Bio::AlignIO->new(
        -format => 'fasta',
        -file   => '219877.cdna.fasta');
  my $alnobj = $alignio->next_aln;

  # Analyze the aligment and get a Tree
  my $tree = $factory->run($alnobj);


Get a Bio::Tree object using raxml given a protein or DNA alignment.


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Please direct usage questions or support issues to the mailing list:

Do not contact the module maintainer directly. Many experienced experts at bioperl-l 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.

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AUTHOR - Brian Osborne



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $treebuilder = Bio::Tools::Run::Phylo::Raxml->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Phylo::Raxml
 Args    : Same as those used to run raxml. For example:

 $factory = Bio::Tools::Run::Phylo::Raxml->new(-p  => 100, -SSE3 => 1) 


 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None


 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory
 Returns:  string
 Args    :


 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysus run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)


 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none


 Title   : quiet
 Usage   : 
 Function: get or set value for 'quiet'
 Example :
 Returns : 
 Args    : the value


 Title   : run
 Usage   : $factory->run($stockholm_file) OR
 Function: Runs Raxml to generate a tree 
 Returns : Bio::Tree::Tree object
 Args    : File name for your input alignment in stockholm format, OR
           Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).


 Title   : _run
 Usage   : Internal function, not to be called directly
 Function: Runs the application
 Returns : Tree object
 Args    : Alignment file name


 Title   : _write_alignfile
 Usage   : Internal function, not to be called directly
 Function: Create an alignment file
 Returns : filename
 Args    : Bio::Align::AlignI


 Title   : _alphabet
 Usage   : my $alphabet = $self->_alphabet;
 Function: Get the alphabet of the input alignment, defaults to 'dna'
 Returns : 'dna' or 'protein'
 Args    : Alignment file


 Title   :  _setparams
 Usage   :  Internal function, not to be called directly    
 Function:  Create parameter inputs for Raxml program
 Example :
 Returns : parameter string to be passed to Raxml
 Args    : name of calling object

Bio::Tools::Run::BaseWrapper methods


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)


Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)


Title : outfile_name Usage : my $outfile = $Raxml->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


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


Title : cleanup Usage : $Raxml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none


Title : io Usage : $obj->io($newval) Function: Gets a Bio::Root::IO object Returns : Bio::Root::IO Args : none