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.IX Title "Bio::Tools::Run::Phylo::Semphy 3pm"
.TH Bio::Tools::Run::Phylo::Semphy 3pm "2021-01-06" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::Semphy \- Wrapper for Semphy
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  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)
\&
\&  # $tree isa Bio::Tree::Tree
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper for running the Semphy application by N. Friedman et a.. You
can get details here: http://compbio.cs.huji.ac.il/semphy/. Semphy is used for
phylogenetic reconstruction (making a tree with branch lengths from an aligned
set of input sequences).
.PP
You can try supplying normal Semphy command-line arguments to \fBnew()\fR, eg.
new(\-hky => 1) or calling arg-named methods (excluding the initial hyphen(s),
eg. \f(CW$factory\fR\->\fBhky\fR\|(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 \fBsemphy_verbose()\fR method.
.PP
You will need to enable this Semphy wrapper to find the Semphy program.
This can be done in (at least) three ways:
.PP
.Vb 4
\& 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} = \*(Aq/home/username/semphy/\*(Aq }
\&    use Bio::Tools::Run::Phylo::Semphy;
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : None
.Ve
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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\*(Aqt make sense in this context):
\&           \-h | \-\-help | \-\-fill\-help
\&           \-s | \-\-sequence
\&           \-t | \-\-tree
\&
\&           To distinguish between Bioperl\*(Aqs \-verbose and the Semphy\*(Aqs \-\-verbose,
\&           you must set Semphy\*(Aqs verbosity with \-semphy_verbose
.Ve
.SS "run"
.IX Subsection "run"
.Vb 10
\& 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.
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 5
\& 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
.Ve