Bio::Tools::Run::Phylo::Semphy(3) Wrapper for Semphy


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


This is a wrapper for running the Semphy application by N. Friedman et a.. You can get details here: 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;


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Please direct usage questions or support issues to the mailing list:

[email protected]

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:

AUTHOR - Sendu Bala

Email [email protected]


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


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


 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


 Title   : run
 Usage   : $result = $factory->run($fasta_align_file);
           $result = $factory->run($align_object);
           $result = $factory->run($fasta_align_file, $newick_tree_file);
           $result = $factory->run($align_object, $tree_object);
           $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
           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.


 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