NAME

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

SYNOPSIS

         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);

DESCRIPTION

       This is a wrapper for running the phyloFit application by Adam Siepel. You can get details
       here: http://compgen.bscb.cornell.edu/~acs/software.html

       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;

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::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

   run
        Title   : run
        Usage   : $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 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
                  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, 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

   _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

perl v5.36.0                                2023-01-2Bio::Tools::Run::Phylo::Phast::PhyloFit(3pm)