The Perl Advent Calendar needs more articles for 2022. Submit your idea today!


Bio::Tools::Run::Phylo::Phast::PhyloFit - Wrapper for phyloFit


  use Bio::Tools::Run::Phylo::Phast::PhyloFit;

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

  # Generate an init.mod file for use by phastCons
  my $init_file = $factory->run($alignment, $tree);


This is a wrapper for running the phyloFit application by Adam Siepel. You can get details here:

Currently the interface is extremely simplified. Only the --tree form of usage is allowed (not --init-model), which means a tree must be supplied with the alignment (to run()). You can try supplying normal phyloFit arguments to new(), or calling arg-named methods (excluding initial hyphens and converting others to underscores, eg. $factory->gaps_as_bases(1) to set the --gaps-as-bases arg).

WARNING: the API may change in the future to allow for greater flexability and access to more phyloFit features.

You will need to enable this PhyloFit wrapper to find the phast programs (at least phyloFit itself). This can be done in (at least) three ways:

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

    export PHASTDIR=/home/username/phast/bin

    In csh/tcsh:

    setenv PHASTDIR /home/username/phast/bin

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

    BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
    use Bio::Tools::Run::Phylo::Phast::PhyloFit;


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.                  - General discussion  - About the mailing lists


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

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



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::Phast::PhyloFit->new()
 Function: creates a new PhyloFit factory
 Returns : Bio::Tools::Run::Phylo::Phast::PhyloFit
 Args    : Most options understood by phastCons can be supplied as key =>
           value pairs. Options that don't normally take a value
           should be given a value of 1. You can type the keys as you would on
           the command line (eg. '--gaps-as-bases' => 1) or with only a single
           hyphen to start and internal hyphens converted to underscores (eg.
           -gaps_as_bases => 1) to avoid having to quote the key.

           These options can NOT be used with this wrapper currently:
           msa_format / i
           out_root / o
           tree / t
           help / h
           lnl / L
           init_model / M
           scale_only / B
           scale_subtree / S
           no_freqs / f
           no_rates / n
           post_probs / P
           expected_subs / X
           expected_total_subs / Z
           column_probs / U
           windows / w
           windows_explicit / v


 Title   : run
 Usage   : $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 phyloFit on an alignment.
 Returns : filename of init.mod file produced
 Args    : The first argument represents an alignment, the second argument
           a species tree.
           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, the alignment sequence names must correspond to node
           ids in the species tree. Multi-word species names should be joined
           with underscores to form the sequence names, eg. Homo_sapiens


 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