NAME

       Bio::Tools::Run::Phylo::Raxml - Bio::Tree getter from DNA alignment through raxml

SYNOPSIS

         # 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);

DESCRIPTION

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

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 one of the Bioperl mailing lists.  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

       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.

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

        http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Brian Osborne

       Email briano@bioteam.net

APPENDIX

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

   new
        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)

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

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

   error_string
        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)

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

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

   run
        Title   : run
        Usage   : $factory->run($stockholm_file) OR
                  $factory->run($align_object)
        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).

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

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

   _alphabet
        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

   _setparams
        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

   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 = $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

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

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