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.IX Title "Bio::Tools::Run::Phylo::Phast::PhyloFit 3pm"
.TH Bio::Tools::Run::Phylo::Phast::PhyloFit 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH NAME
Bio::Tools::Run::Phylo::Phast::PhyloFit \- Wrapper for phyloFit
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 1
\&  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, $tree);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
This is a wrapper for running the phyloFit application by Adam Siepel. You
can get details here: http://compgen.bscb.cornell.edu/~acs/software.html
.PP
Currently the interface is extremely simplified. Only the \-\-tree form of usage
is allowed (not \-\-init\-model), which means a tree must be supplied with the
alignment (to \fBrun()\fR). You can try supplying normal phyloFit arguments to \fBnew()\fR,
or calling arg-named methods (excluding initial hyphens and converting others
to underscores, eg. \f(CW$factory\fR\->\fBgaps_as_bases\fR\|(1) to set the \-\-gaps\-as\-bases arg).
.PP
WARNING: the API may change in the future to allow for greater flexability and
access to more phyloFit features.
.PP
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:
.PP
.Vb 4
\& 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} = \*(Aq/home/username/phast/bin\*(Aq }
\&    use Bio::Tools::Run::Phylo::Phast::PhyloFit;
.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 10
\& 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\*(Aqt normally take a value
\&           should be given a value of 1. You can type the keys as you would on
\&           the command line (eg. \*(Aq\-\-gaps\-as\-bases\*(Aq => 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
.Ve
.SS run
.IX Subsection "run"
.Vb 10
\& 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
.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