Provided by: libbio-perl-run-perl_1.7.1-3_all bug




         # 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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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