Provided by: libbio-perl-run-perl_1.7.3-3_all bug




         # Build a FastTree factory
         $factory = Bio::Tools::Run::Phylo::FastTree->new(-quiet => 1,
                                                          -fastest => 1);
         # 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 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::FastTree->new();
        Function: Constructor
        Returns : Bio::Tools::Run::Phylo::FastTree
        Args    : -outfile_name => $outname

        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   : run
        Usage   : $factory->run($stockholm_file) OR
        Function: Runs FastTree 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 FastTree program
        Example :
        Returns : parameter string to be passed to FastTree
        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)
        Returns : value of save_tempfiles
        Args    : newvalue (optional)

        Title   : outfile_name
        Usage   : my $outfile = $FastTree->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   : $FastTree->cleanup();
        Function: Will cleanup the tempdir directory
        Returns : none
        Args    : none

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