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.IX Title "Bio::Tools::Run::Phylo::FastTree 3pm"
.TH Bio::Tools::Run::Phylo::FastTree 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH NAME
Bio::Tools::Run::Phylo::FastTree \- Bio::Tree getter from DNA alignment
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 8
\&  # Build a FastTree factory
\&  $factory = Bio::Tools::Run::Phylo::FastTree\->new(\-quiet => 1,
\&                                                   \-fastest => 1);
\&  # Get an alignment
\&  my $alignio = Bio::AlignIO\->new(
\&        \-format => \*(Aqfasta\*(Aq,
\&        \-file   => \*(Aq219877.cdna.fasta\*(Aq);
\&  my $alnobj = $alignio\->next_aln;
\&
\&  # Analyze the aligment and get a Tree
\&  my $tree = $factory\->run($alnobj);
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Get a Bio::Tree object given a protein or DNA alignment.
.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 one
of the Bioperl mailing lists.  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
Do not contact the module maintainer directly. Many experienced experts 
at bioperl-l 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
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 \-  Brian Osborne"
.IX Header "AUTHOR - Brian Osborne"
Email briano@bioteam.net
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS new
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $treebuilder = Bio::Tools::Run::Phylo::FastTree\->new();
\& Function: Constructor
\& Returns : Bio::Tools::Run::Phylo::FastTree
\& Args    : \-outfile_name => $outname
.Ve
.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
\& Returns:  string
\& Args    :
.Ve
.SS error_string
.IX Subsection "error_string"
.Vb 5
\& Title   : error_string
\& Usage   : $obj\->error_string($newval)
\& Function: Where the output from the last analysus run is stored.
\& Returns : value of error_string
\& Args    : newvalue (optional)
.Ve
.SS version
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS run
.IX Subsection "run"
.Vb 7
\& Title   : run
\& Usage   : $factory\->run($stockholm_file) OR
\&           $factory\->run($align_object)
\& Function: Runs FastTree to generate a tree 
\& Returns : Bio::Tree::Tree object
\& Args    : File name for your input alignment in stockholm format, OR
\&           Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   : _run
\& Usage   : Internal function, not to be called directly
\& Function: Runs the application
\& Returns : Tree object
\& Args    : Alignment file name
.Ve
.SS _write_alignfile
.IX Subsection "_write_alignfile"
.Vb 5
\& Title   : _write_alignfile
\& Usage   : Internal function, not to be called directly
\& Function: Create an alignment file
\& Returns : filename
\& Args    : Bio::Align::AlignI
.Ve
.SS _alphabet
.IX Subsection "_alphabet"
.Vb 5
\& Title   : _alphabet
\& Usage   : my $alphabet = $self\->_alphabet;
\& Function: Get the alphabet of the input alignment, defaults to \*(Aqdna\*(Aq
\& Returns : \*(Aqdna\*(Aq or \*(Aqprotein\*(Aq
\& Args    : Alignment file
.Ve
.SS _setparams
.IX Subsection "_setparams"
.Vb 6
\& Title   :  _setparams
\& Usage   :  Internal function, not to be called directly    
\& Function:  Create parameter inputs for FastTree program
\& Example :
\& Returns : parameter string to be passed to FastTree
\& Args    : name of calling object
.Ve
.SH "Bio::Tools::Run::BaseWrapper methods"
.IX Header "Bio::Tools::Run::BaseWrapper methods"
.SS no_param_checks
.IX Subsection "no_param_checks"
.Vb 6
\& Title   : no_param_checks
\& Usage   : $obj\->no_param_checks($newval)
\& Function: Boolean flag as to whether or not we should
\&           trust the sanity checks for parameter values  
\& Returns : value of no_param_checks
\& Args    : newvalue (optional)
.Ve
.SS save_tempfiles
.IX Subsection "save_tempfiles"
.Vb 5
\& Title   : save_tempfiles
\& Usage   : $obj\->save_tempfiles($newval)
\& Function: 
\& Returns : value of save_tempfiles
\& Args    : newvalue (optional)
.Ve
.SS outfile_name
.IX Subsection "outfile_name"
.Vb 6
\& Title   : outfile_name
\& Usage   : my $outfile = $FastTree\->outfile_name();
\& Function: Get/Set the name of the output file for this run
\&           (if you wanted to do something special)
\& Returns : string
\& Args    : [optional] string to set value to
.Ve
.SS tempdir
.IX Subsection "tempdir"
.Vb 5
\& Title   : tempdir
\& Usage   : my $tmpdir = $self\->tempdir();
\& Function: Retrieve a temporary directory name (which is created)
\& Returns : string which is the name of the temporary directory
\& Args    : none
.Ve
.SS cleanup
.IX Subsection "cleanup"
.Vb 5
\& Title   : cleanup
\& Usage   : $FastTree\->cleanup();
\& Function: Will cleanup the tempdir directory
\& Returns : none
\& Args    : none
.Ve
.SS io
.IX Subsection "io"
.Vb 5
\& Title   : io
\& Usage   : $obj\->io($newval)
\& Function:  Gets a L<Bio::Root::IO> object
\& Returns : L<Bio::Root::IO>
\& Args    : none
.Ve