NAME

       Bio::Tools::Run::Phylo::Semphy - Wrapper for Semphy

SYNOPSIS

         use Bio::Tools::Run::Phylo::Semphy;

         # Make a Semphy factory
         $factory = Bio::Tools::Run::Phylo::Semphy->new();

         # Run Semphy with an alignment
         my $tree = $factory->run($alignfilename);

         # or with alignment object
         $tree = $factory->run($bio_simplalign);

         # you can supply an initial tree as well, which can be a newick tree file,
         # Bio::Tree::Tree object...
         $tree = $factory->run($bio_simplalign, $tree_obj);

         # ... or Bio::DB::Taxonomy object
         $tree = $factory->run($bio_simplalign, $bio_db_taxonomy);

         # (mixtures of all the above are possible)

         # $tree isa Bio::Tree::Tree

DESCRIPTION

       This is a wrapper for running the Semphy application by N. Friedman et a.. You can get
       details here: http://compbio.cs.huji.ac.il/semphy/. Semphy is used for phylogenetic
       reconstruction (making a tree with branch lengths from an aligned set of input sequences).

       You can try supplying normal Semphy command-line arguments to new(), eg.  new(-hky => 1)
       or calling arg-named methods (excluding the initial hyphen(s), eg. $factory->hky(1) to set
       the --hky switch to true).  Note that Semphy args are case-sensitive. To distinguish
       between Bioperl's -verbose and the Semphy's --verbose, you must set Semphy's verbosity
       with -semphy_verbose or the semphy_verbose() method.

       You will need to enable this Semphy wrapper to find the Semphy program.  This can be done
       in (at least) three ways:

        1. Make sure the Semphy executable is in your path.
        2. Define an environmental variable SEMPHYDIR which is a
           directory which contains the Semphy application:
           In bash:

           export SEMPHYDIR=/home/username/semphy/

           In csh/tcsh:

           setenv SEMPHYDIR /home/username/semphy

        3. Include a definition of an environmental variable SEMPHYDIR in
           every script that will use this Semphy wrapper module, e.g.:

           BEGIN { $ENV{SEMPHYDIR} = '/home/username/semphy/' }
           use Bio::Tools::Run::Phylo::Semphy;

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

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

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   : $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, obtained from ENV variable.
        Returns : string
        Args    : None

   new
        Title   : new
        Usage   : $factory = Bio::Tools::Run::Phylo::Semphy->new()
        Function: creates a new Semphy factory
        Returns : Bio::Tools::Run::Phylo::Semphy
        Args    : Most options understood by Semphy can be supplied as key =>
                  value pairs, with a true value for switches.

                  These options can NOT be used with this wrapper (they are handled
                  internally or don't make sense in this context):
                  -h | --help | --fill-help
                  -s | --sequence
                  -t | --tree

                  To distinguish between Bioperl's -verbose and the Semphy's --verbose,
                  you must set Semphy's verbosity with -semphy_verbose

   run
        Title   : run
        Usage   : $result = $factory->run($fasta_align_file);
                  -or-
                  $result = $factory->run($align_object);
                  -or-
                  $result = $factory->run($fasta_align_file, $newick_tree_file);
                  -or-
                  $result = $factory->run($align_object, $tree_object);
                  -or-
                  $result = $factory->run($align_object, $db_taxonomy_object);
        Function: Runs Semphy on an alignment.
        Returns : Bio::Tree::Tree
        Args    : The first argument represents an alignment, the second (optional)
                  argument a species tree (to set an initial tree: normally the -t
                  option to Semphy).
                  The alignment can be provided as a multi-fasta format alignment
                  filename, or a Bio::Align::AlignI compliant object (eg. a
                  Bio::SimpleAlign).
                  The species tree can be provided as a newick format tree filename
                  or a Bio::Tree::TreeI compliant object. Alternatively a
                  Bio::DB::Taxonomy object can be supplied, in which case the species
                  tree will be generated by using the alignment sequence names as
                  species names and looking for those in the supplied database.

                  In all cases where an initial tree was supplied, the alignment
                  sequence names must correspond to node ids in the species tree.

   _setparams
        Title   : _setparams
        Usage   : Internal function, not to be called directly
        Function: Creates a string of params to be used in the command string
        Returns : string of params
        Args    : alignment and tree file names